Difference between revisions of "Preparing the protein"

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==Modifying the PDB file==
 
==Modifying the PDB file==
 
   
 
   
*prepare <tt>rec.pdb</tt>  by removing all lines that do not commence with 'ATOM', the chain column, all columns to the right of the z-coordinate and the TER statements.   
+
*prepare <tt>rec.pdb</tt>  by removing all lines that do not commence with 'ATOM', all columns to the right of the z-coordinate and the TER statements.   
*treat all selenomethionines (MSE) as methionines (MET) by replacing the selenium atom (SE&curren;) with sulphur   (&curren;SD). Be careful about the correct alignment!   
+
*treat all selenomethionines (MSE) as methionines (MET) by replacing the selenium atom (SE&curren;) with sulphur (&curren;SD). Be careful about the correct alignment!   
*atom enumeration does not matter, so don't bother to renumber   after any of the following steps. Unique numbers are a good idea,   presumably.   
+
*atom enumeration does not matter, so don't bother to renumber after any of the following steps. Unique numbers are a good idea, presumably.   
*select the protonation states of HIS residues to be either &delta;- (rename residue to HID), &epsilon;- (rename residue to HIE) or doubly protonated (rename residue to HIP). HIS on the surface should be HIP. HIS residues coordinating   the metal ions should have their protons pointing away from the   ions. Base your decision on the immediate environment of the HIS residue: are there potential hydrogen bonds that can be formed?; are there charged residues close by?; would a certain protonation lead to clashes with other residues?; etc.
+
*select the protonation states of HIS residues to be either &delta;- (rename residue to HID), &epsilon;- (rename residue to HIE) or doubly protonated (rename residue to HIP). HIS on the surface should be HIP. HIS residues coordinating the metal ions should have their protons pointing away from the ions. Base your decision on the immediate environment of the HIS residue: are there potential hydrogen bonds that can be formed?; are there charged residues close by?; would a certain protonation lead to clashes with other residues?; etc.
*AH: the carboxylated LYS of subtype I is CYK, but this is not   tolerated by <tt>startdockblaster5</tt> , so store and delete the 3   surplus atoms and call the residue LYS.   
+
*AH: the carboxylated LYS of subtype I is CYK, but this is not tolerated by <tt>startdockblaster5</tt> , so store and delete the 3 surplus atoms and call the residue LYS.   
*AH: the more buried metal ion is ZB (charge 1.4), the other one ZA   (charge 1.3). Atom names are right-aligned!
+
*AH: the more buried metal ion is ZB (charge 1.4), the other one ZA (charge 1.3). Atom names are right-aligned!
  
 
==Running startdockblaster5==
 
==Running startdockblaster5==
 
    
 
    
*generate the file <tt>xtal-lig.pdb</tt> , which should only contain   atoms of the MMFF. Prepare it in the same way as above: remove the    chain column, all columns to the right of the z-coordinate and the   TER statements.
+
*generate the file <tt>xtal-lig.pdb</tt> , which should only contain atoms of the molecular modeling force field. Prepare it in the same way as above: remove all columns to the right of the z-coordinate and the TER statements. Change HETATM to ATOM.
*generate the files <tt>.only_spheres</tt> and &ndash; in case you   would like the matching spheres to be based on the heavy atoms in <tt>xtal-lig.pdb</tt> &ndash; <tt>.useligsph</tt> and write `on' to the   latter. Be careful not to add blank lines at the end, this will not   be understood by <tt>makespheres2.pl</tt> . In any case, the entry in   <tt>.useligsph</tt>  will be ignored by <tt>makespheres1.pl</tt> .   
+
*generate the files <tt>.only_spheres</tt> and &ndash; in case you would like the matching spheres to be based on the heavy atoms in <tt>xtal-lig.pdb</tt> &ndash; <tt>.useligsph</tt> and write `on' to the latter. Be careful not to add blank lines at the end, this will not be understood by <tt>makespheres2.pl</tt> . In any case, the entry in <tt>.useligsph</tt>  will be ignored by <tt>makespheres1.pl</tt> .   
*on sgehead (or, as of [[dock67]], on any machine), run <tt>startdockblaster5</tt>  to set up the data structure and copy all relevant files. It is a good idea to use csh and to <tt>source .login</tt> beforehand.   
+
*on sgehead (or, as of [[dock67]], on any machine), run <tt>startdockblaster5</tt>  to set up the data structure and copy all relevant files. It is a good idea to use csh and to <tt>source .login</tt> beforehand.   
*if <tt>startdockblaster5</tt>  doesn't finish for any obvious reason and with no clear error message, or <tt>rec.crg</tt> has very funny hydrogen placements, make sure that you have no non-printing characters in <tt>rec.pdb</tt> or <tt>xtal-lig.pdb</tt>. Do that by running your file through <tt>pc2unix rec.pdb</tt>. Check that your file is clean by looking at it with <tt>od -c rec.pdb | less </tt>. The only character with a backslash should be \n &mdash; you should see no \t, \r, etc. If this doesn't solve the problem, your best bet is to   reprepare <tt>rec.pdb</tt> and <tt>xtal-lig.pdb</tt> from scratch &mdash; it is   likely that there are some blanks or hidden characters that are   causing the problems.   
+
*if <tt>startdockblaster5</tt>  doesn't finish for any obvious reason and with no clear error message, or <tt>rec.crg</tt> has very funny hydrogen placements, make sure that you have no non-printing characters in <tt>rec.pdb</tt> or <tt>xtal-lig.pdb</tt>. Do that by running your file through <tt>pc2unix rec.pdb</tt>. Check that your file is clean by looking at it with <tt>od -c rec.pdb | less </tt>. The only character with a backslash should be \n &mdash; you should see no \t, \r, etc. If this doesn't solve the problem, your best bet is to re-prepare <tt>rec.pdb</tt> and <tt>xtal-lig.pdb</tt> from scratch &mdash; it is likely that there are some blanks or hidden characters that are causing the problems.   
*check the files <tt>stdout</tt>  and <tt>stderr</tt>  after the    run for potential mistakes and error messages. Furthermore, verify   that <tt>rec.crg</tt> still contains ''all'' atoms.   
+
*Take any WARNING messages emitted seriously, and continue only if you know why each one is there. Furthermore, verify that <tt>rec.crg</tt> still contains ''all'' atoms.   
*if you do not want to do anything special with the protein, like   tarting some residues or modifying the spheres, go directly to chapter [[Running DOCK|3]].
+
*if you do not want to do anything special with the protein, like tarting some residues or modifying the spheres, go directly to chapter [[Running DOCK|3]].
  
 
==Removing and modifying files==
 
==Removing and modifying files==
 
    
 
    
*go to <tt>./grids</tt>  and remove the surplus files from this   directory (some would cause error messages from the subsequent   programs):<br><tt>rm -f PDBPARM chem.* distmap.box  distmap    distmap.log rec+sph.phi solvmap tart.txt OUT*</tt>
+
*go to <tt>./grids</tt>  and remove the surplus files from this directory (some would cause error messages from the subsequent programs):<br><tt>rm -f PDBPARM chem.* rec+sph.phi solvmap_sev tart.txt OUT*</tt>
*modify <tt>rec.crg</tt>:    
+
*modify <tt>rec.crg</tt>:  
*
+
**AH: CYK: put the three missing atoms, delete the surplus hydrogens specific for LYS and rename the carboxylated lysine residue CYK.   
*AH: CYK: put the three missing atoms, delete the surplus hydrogens specific for LYS and rename the carboxylated lysine residue CYK.   
+
**remove all TER statements that might have been added.   
*
+
**AH: set the atom names of the metal ions to ZA and ZB and the residue name to ZN.   
*remove all TER statements that might have been added.   
+
**take care of disulfide bonds. Remove the thiol hydrogens (if they have been added) and change the residue name from CYS to CYX.   
*
+
*look at the <tt>box</tt> and maybe move it, so that the ligands won't stick out. Modify the 'center' and 'coordinates' statement in the preamble.   
*AH: set the atom names of the metal ions to ZA and ZB and the   residue name to ZN.   
+
*all residues and atoms have to be listed in <tt>prot.table.ambcrg.ambH</tt> and <tt>vdw.parms.amb.mindock</tt>, respectively &rArr; do not tart any residues in this file!
*
 
*take care of disulfide bonds. Remove the thiol hydrogens (if   they have been added) and change the residue name from CYS to CYX.   
 
*
 
*look at the <tt>box</tt> and maybe move it, so that the ligands   won't stick out. Modify the 'center' and 'coordinates' statement in   the preamble.   
 
*
 
*all residues and atoms have to be listed in <tt>prot.table.ambcrg.ambH</tt> and <tt>vdw.parms.amb.mindock</tt>, respectively &rArr; do not tart any residues in this file!  
 
  
 
==Running <tt>[[chemgrid]]</tt> ==
 
==Running <tt>[[chemgrid]]</tt> ==
 
    
 
    
*run <tt>chemgrid</tt> and check <tt>OUTPARM</tt> for the correct charges of all residues.   
+
*run <tt>chemgrid</tt> and check <tt>OUTPARM</tt> for the correct van der Waals parameters of all residues.   
*grep for <tt>0.000</tt>  in <tt>PDBPARM</tt>: if any atom has this   value in the 3<sup>rd</sup> and 4<sup>th</sup> column, it has not been   recognized by <tt>chemgrid</tt>  (because it is not listed in <tt>prot.table.ambcrg.ambH</tt>) and is thus ''ignored'' in the van der   Waals-maps. There will be no other errors, the docking will finish   showing some "bumping" ligands which have extremely favorable   energies (&le; -200).
+
*grep for <tt>0.000</tt>  in <tt>PDBPARM</tt>: if any atom has this value in the 3<sup>rd</sup> and 4<sup>th</sup> column, it has not been recognized by <tt>chemgrid</tt>  (because it is not listed in <tt>prot.table.ambcrg.ambH</tt>) and is thus ''ignored'' in the van der Waals-maps. There will be no other errors, the docking will finish showing some "bumping" ligands which have extremely favorable energies (&le; -200).
*Another sign of a problem with atomic radii are any 'WARNING' issued in OUTPARM
+
*Another sign of a problem with atomic radii are any 'WARNING's issued in OUTPARM
*if one has to run <tt>chemgrid</tt>  again, remove <tt>PDBPARM OUTPARM OUTCHEM</tt> and <tt>chem.*</tt>.
+
*if one has to run <tt>chemgrid</tt>  again, first remove <tt>PDBPARM OUTPARM OUTCHEM</tt> and <tt>chem.*</tt>.
 
 
==Running <tt>distmap</tt> ==
 
 
* the default is to run <tt>distmap</tt> on <tt>rec.crg</tt>. If you modified this file, rerun by simply typing <tt>distmap</tt>.
 
* AH: cp <tt>rec.crg</tt> to <tt>rec-dist.crg</tt>  and remove the Zn atoms in the latter file (otherwise there will be lots of bumping ligands). Edit <tt>INDIST</tt> to update the filename.
 
*run <tt>distmap</tt>
 
  
 
==Tarting the protein==
 
==Tarting the protein==
 
    
 
    
*cp <tt>rec.crg</tt> to <tt>rec+sph.crg</tt> and continue with the latter file.
+
*cp <tt>rec.crg</tt> to <tt>rec+sph.crg</tt> and continue with the latter file.
 
* tarted residues can be found in <tt>$DOCK_BASE/scripts/grids</tt>, they are the files with the extension <tt>prot2</tt>.
 
* tarted residues can be found in <tt>$DOCK_BASE/scripts/grids</tt>, they are the files with the extension <tt>prot2</tt>.
* take care that the format of the <tt>.prot2</tt> file is consistent with the format in the <tt>amb.crg.oxt</tt> file, e.g., that there is no leading space before an atom name etc.
+
* add the relevant resides to the bottom of your <tt>prot.table.ambcrg.ambH</tt> file, being very precise to match the current formatting
*AH: select the appropriate version of <tt>amb.crg.oxt</tt> depending on   the subtype. Files are called <tt>amb.crg.oxt.N</tt> , where <tt>N</tt> can   be <tt>I, III</tt> or <tt>VI</tt> .   
+
* generate the new <tt>amb.crg.oxt</tt> from the edited <tt>prot.table.ambcrg.ambH</tt> using:<br><tt>$mud/prot2crg.py < prot.table.ambcrg.ambH > amb.crg.oxt</tt>
*AH: edit the residues in the binding site (i.e., all residues   complexing the metal ions in the binding site), so that their   names conform to the names of the modified residues in <tt>amb.crg.oxt.N</tt>   
+
*AH: select the appropriate version of <tt>amb.crg.oxt</tt> depending on the subtype. Files are called <tt>amb.crg.oxt.N</tt>, where <tt>N</tt> can be <tt>I, III</tt> or <tt>VI</tt>.   
*tart the residues that are in contact with a crystallographic   ligand, if any.   
+
*AH: edit the residues in the binding site (i.e., all residues complexing the metal ions in the binding site), so that their names conform to the names of the modified residues in <tt>amb.crg.oxt.N</tt>   
*AH: check that ZA and ZB, respectively (left-aligned in the atom   column), have corresponding entries in <tt>amb.crg.oxt.N</tt>  and <tt>vdw.siz</tt>.
+
*optionally tart the residues that are in contact with a crystallographic ligand, if any.   
 +
*AH: check that ZA and ZB, respectively (left-aligned in the atom column), have corresponding entries in <tt>amb.crg.oxt.N</tt>  and <tt>vdw.siz</tt>.
  
==Modifying the spheres==
+
==Modifying the Delphi spheres==
 
    
 
    
*load <tt>match1.sph.pdb</tt> (i.e., the DelPhi spheres).   
+
*load <tt>match1.sph.pdb</tt> (i.e., the DelPhi spheres).   
 
*delete the spheres that are too close to the solvent.   
 
*delete the spheres that are too close to the solvent.   
*(AH:) add spheres so that there is one sphere ''between'' the metals, several spheres ''around'' the metals and some spheres   close to polar residues.   
+
*(AH:) add spheres so that there is one sphere ''between'' the metals, several spheres ''around'' the metals and some spheres close to polar residues.   
 
*a good number for DelPhi spheres is 120.   
 
*a good number for DelPhi spheres is 120.   
*append the spheres to the end of <tt>rec+sph.crg</tt> and put a TER   statement after each sphere. Don't use tabs for whitespace, can   cause problems with DelPhi!   
+
*append the spheres to the end of <tt>rec.crg</tt> to make <tt>rec+sph.crg</tt> and put a TER statement after each sphere. Don't use tabs for whitespace, can cause problems with DelPhi!   
*do the same for <tt>match2.sph.pdb</tt> (i.e., the matching    spheres); put at least one sphere between the metals and increase    the sampling in the region around the metal ions by putting some    spheres there. If you selected <tt>.useligsph</tt> . be careful not to   move any spheres based on the ligand atoms.   
+
 
*a good number for matching spheres is 40.   
+
==Modifying the Matching spheres==
*run <tt>pdb_to_spheres.py matchN.sph.pdb matchN.sph</tt> to   generate the files that will be read by DelPhi/[[DOCK]].
+
 
*if desired, run <tt>colorspheres.pl sph/match2.sph</tt> in the   parent directory of the docking run (i.e., <tt>..</tt> to <tt>grids</tt> )   to put some color on your spheres.   
+
*load <tt>match2.sph.pdb</tt> for sparse initial spheres or <tt>match3.sph.pdb</tt> denser spheres.
*in any case, put the preamble ("DOCK 5.2 ligand_atoms...")    into <tt>match2.sph</tt> .
+
*If you selected <tt>.useligsph</tt> be careful not to move any spheres based on the ligand atoms.   
 +
*(AH:) put at least one sphere between the metals and increase the sampling in the region around the metal ions by putting some spheres there.
 +
*a good number for matching spheres is 50-60.   
 +
*run <tt>pdbtosph matchN.sph.pdb mysph.sph</tt> to generate the files that will be read by [[DOCK]].  
 +
*if color matching is desired, run <tt>colorspheres.pl sph/match2.sph</tt> in the parent directory of the docking run (i.e., <tt>..</tt> to <tt>sph</tt> ) to put some color on your spheres.   
 +
*run <tt>cat $mud/header.sph match2.sph</tt> .
  
 
==Running <tt>[http://bcr.musc.edu/manuals/delphi.htm DelPhi]</tt> ==
 
==Running <tt>[http://bcr.musc.edu/manuals/delphi.htm DelPhi]</tt> ==
 
+
 
*if necessary, modify <tt>delphi.com</tt> so that all the paths and file names are   appropriate.   
+
With the Makefile all someone needs to do is go up one directory and run the make command by typing:
 +
> cd ../
 +
> make grids/rec+sph.phi
 +
 
 +
And the Make file will do the work.
 +
 
 +
Old stuff (we might want to get ride of this):
 +
 
 +
*if you changed rec+sph.crg above, you need to run Delphi 
 +
*if necessary, modify <tt>delphi.com</tt> so that all the paths and file names are appropriate.   
 
*run <tt>delphi.com > delphi.log</tt>  and check the output.
 
*run <tt>delphi.com > delphi.log</tt>  and check the output.
 
*any 'WARNING' in the log is an indication that some atomic charges might not be correct.
 
*any 'WARNING' in the log is an indication that some atomic charges might not be correct.
  
==Running <tt>[[solvmap]]</tt> ==
+
==Running <tt>[[newsolv.sev]]</tt> ==
 
    
 
    
*check that all atoms are present in <tt>rec.crg</tt> and run <tt>solvmap</tt> .
+
*if you changed rec.crg or the box above, you need to run newsolv.sev 
*after the run, make sure that the file <tt>solvmap</tt> contains '''no''' blank lines.
+
*check that all atoms are present in <tt>rec.crg</tt> and run <tt>newsolv.sev</tt> .
  
 
[[Category:Manual_DOCK]]
 
[[Category:Manual_DOCK]]
 
[[Category:Tutorials]]
 
[[Category:Tutorials]]

Latest revision as of 23:15, 28 December 2012

Preparing the protein

Items which are prefixed with 'AH' are relevant for docking HEIs to amidohydrolases and can safely be ignored for most metal-free proteins.

Modifying the PDB file

  • prepare rec.pdb by removing all lines that do not commence with 'ATOM', all columns to the right of the z-coordinate and the TER statements.
  • treat all selenomethionines (MSE) as methionines (MET) by replacing the selenium atom (SE¤) with sulphur (¤SD). Be careful about the correct alignment!
  • atom enumeration does not matter, so don't bother to renumber after any of the following steps. Unique numbers are a good idea, presumably.
  • select the protonation states of HIS residues to be either δ- (rename residue to HID), ε- (rename residue to HIE) or doubly protonated (rename residue to HIP). HIS on the surface should be HIP. HIS residues coordinating the metal ions should have their protons pointing away from the ions. Base your decision on the immediate environment of the HIS residue: are there potential hydrogen bonds that can be formed?; are there charged residues close by?; would a certain protonation lead to clashes with other residues?; etc.
  • AH: the carboxylated LYS of subtype I is CYK, but this is not tolerated by startdockblaster5 , so store and delete the 3 surplus atoms and call the residue LYS.
  • AH: the more buried metal ion is ZB (charge 1.4), the other one ZA (charge 1.3). Atom names are right-aligned!

Running startdockblaster5

  • generate the file xtal-lig.pdb , which should only contain atoms of the molecular modeling force field. Prepare it in the same way as above: remove all columns to the right of the z-coordinate and the TER statements. Change HETATM to ATOM.
  • generate the files .only_spheres and – in case you would like the matching spheres to be based on the heavy atoms in xtal-lig.pdb.useligsph and write `on' to the latter. Be careful not to add blank lines at the end, this will not be understood by makespheres2.pl . In any case, the entry in .useligsph will be ignored by makespheres1.pl .
  • on sgehead (or, as of dock67, on any machine), run startdockblaster5 to set up the data structure and copy all relevant files. It is a good idea to use csh and to source .login beforehand.
  • if startdockblaster5 doesn't finish for any obvious reason and with no clear error message, or rec.crg has very funny hydrogen placements, make sure that you have no non-printing characters in rec.pdb or xtal-lig.pdb. Do that by running your file through pc2unix rec.pdb. Check that your file is clean by looking at it with od -c rec.pdb | less . The only character with a backslash should be \n — you should see no \t, \r, etc. If this doesn't solve the problem, your best bet is to re-prepare rec.pdb and xtal-lig.pdb from scratch — it is likely that there are some blanks or hidden characters that are causing the problems.
  • Take any WARNING messages emitted seriously, and continue only if you know why each one is there. Furthermore, verify that rec.crg still contains all atoms.
  • if you do not want to do anything special with the protein, like tarting some residues or modifying the spheres, go directly to chapter 3.

Removing and modifying files

  • go to ./grids and remove the surplus files from this directory (some would cause error messages from the subsequent programs):
    rm -f PDBPARM chem.* rec+sph.phi solvmap_sev tart.txt OUT*
  • modify rec.crg:
    • AH: CYK: put the three missing atoms, delete the surplus hydrogens specific for LYS and rename the carboxylated lysine residue CYK.
    • remove all TER statements that might have been added.
    • AH: set the atom names of the metal ions to ZA and ZB and the residue name to ZN.
    • take care of disulfide bonds. Remove the thiol hydrogens (if they have been added) and change the residue name from CYS to CYX.
  • look at the box and maybe move it, so that the ligands won't stick out. Modify the 'center' and 'coordinates' statement in the preamble.
  • all residues and atoms have to be listed in prot.table.ambcrg.ambH and vdw.parms.amb.mindock, respectively ⇒ do not tart any residues in this file!

Running chemgrid

  • run chemgrid and check OUTPARM for the correct van der Waals parameters of all residues.
  • grep for 0.000 in PDBPARM: if any atom has this value in the 3rd and 4th column, it has not been recognized by chemgrid (because it is not listed in prot.table.ambcrg.ambH) and is thus ignored in the van der Waals-maps. There will be no other errors, the docking will finish showing some "bumping" ligands which have extremely favorable energies (≤ -200).
  • Another sign of a problem with atomic radii are any 'WARNING's issued in OUTPARM
  • if one has to run chemgrid again, first remove PDBPARM OUTPARM OUTCHEM and chem.*.

Tarting the protein

  • cp rec.crg to rec+sph.crg and continue with the latter file.
  • tarted residues can be found in $DOCK_BASE/scripts/grids, they are the files with the extension prot2.
  • add the relevant resides to the bottom of your prot.table.ambcrg.ambH file, being very precise to match the current formatting
  • generate the new amb.crg.oxt from the edited prot.table.ambcrg.ambH using:
    $mud/prot2crg.py < prot.table.ambcrg.ambH > amb.crg.oxt
  • AH: select the appropriate version of amb.crg.oxt depending on the subtype. Files are called amb.crg.oxt.N, where N can be I, III or VI.
  • AH: edit the residues in the binding site (i.e., all residues complexing the metal ions in the binding site), so that their names conform to the names of the modified residues in amb.crg.oxt.N
  • optionally tart the residues that are in contact with a crystallographic ligand, if any.
  • AH: check that ZA and ZB, respectively (left-aligned in the atom column), have corresponding entries in amb.crg.oxt.N and vdw.siz.

Modifying the Delphi spheres

  • load match1.sph.pdb (i.e., the DelPhi spheres).
  • delete the spheres that are too close to the solvent.
  • (AH:) add spheres so that there is one sphere between the metals, several spheres around the metals and some spheres close to polar residues.
  • a good number for DelPhi spheres is 120.
  • append the spheres to the end of rec.crg to make rec+sph.crg and put a TER statement after each sphere. Don't use tabs for whitespace, can cause problems with DelPhi!

Modifying the Matching spheres

  • load match2.sph.pdb for sparse initial spheres or match3.sph.pdb denser spheres.
  • If you selected .useligsph be careful not to move any spheres based on the ligand atoms.
  • (AH:) put at least one sphere between the metals and increase the sampling in the region around the metal ions by putting some spheres there.
  • a good number for matching spheres is 50-60.
  • run pdbtosph matchN.sph.pdb mysph.sph to generate the files that will be read by DOCK.
  • if color matching is desired, run colorspheres.pl sph/match2.sph in the parent directory of the docking run (i.e., .. to sph ) to put some color on your spheres.
  • run cat $mud/header.sph match2.sph .

Running DelPhi

With the Makefile all someone needs to do is go up one directory and run the make command by typing:

> cd ../
> make grids/rec+sph.phi

And the Make file will do the work.

Old stuff (we might want to get ride of this):

  • if you changed rec+sph.crg above, you need to run Delphi
  • if necessary, modify delphi.com so that all the paths and file names are appropriate.
  • run delphi.com > delphi.log and check the output.
  • any 'WARNING' in the log is an indication that some atomic charges might not be correct.

Running newsolv.sev

  • if you changed rec.crg or the box above, you need to run newsolv.sev
  • check that all atoms are present in rec.crg and run newsolv.sev .