http://wiki.docking.org/index.php?title=Solvgrid&feed=atom&action=history
Solvgrid - Revision history
2024-03-28T17:57:47Z
Revision history for this page on the wiki
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http://wiki.docking.org/index.php?title=Solvgrid&diff=6850&oldid=prev
Frodo at 22:33, 12 March 2014
2014-03-12T22:33:23Z
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Frodo
http://wiki.docking.org/index.php?title=Solvgrid&diff=4392&oldid=prev
Therese: 3 revisions
2012-10-08T20:32:24Z
<p>3 revisions</p>
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Therese
http://wiki.docking.org/index.php?title=Solvgrid&diff=4391&oldid=prev
JohnIrwin at 19:42, 20 September 2007
2007-09-20T19:42:49Z
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JohnIrwin
http://wiki.docking.org/index.php?title=Solvgrid&diff=4390&oldid=prev
JohnIrwin at 19:42, 20 September 2007
2007-09-20T19:42:04Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:42, 20 September 2007</td>
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JohnIrwin
http://wiki.docking.org/index.php?title=Solvgrid&diff=4389&oldid=prev
JohnIrwin at 23:02, 19 September 2006
2006-09-19T23:02:27Z
<p></p>
<p><b>New page</b></p><div>3.2.3 SOLVGRID<br />
<br />
AUTHOR Kaushik Raha<br />
<br />
DESCRIPTION:<br />
<br />
The solvgrid program creates bulk (or receptor) and explicit (or ligand) desolvation grids using the occupancy desolvation method (Luty et. al., J. Comp. Chem, 1995; Verkhiver et. al., J. Mol. Recog., 1999). The occupancy desolvation method is phenomenonlogical in nature where desolvation energy can be described pairwise additively. The desolvation energy due to interaction between a ligand atom and receptor atom can be calculated as the solvent affinity of a ligand atom weighted by the volume of the solvent displaced from the receptor atom due to binding and vice versa. Thus,<br />
<br />
Edsol = Si øDES,EXPL(xi) + fi øDES,BULK(xi)<br />
<br />
Where the mobile atom i, has a solvation affinity of Si and a fragmental volume of fi. The solvent affinity of the ligand atom is calculated as:<br />
<br />
lig_atm_sol<br />
<br />
Where qi is the charge on the ligand atom i, and alpha and beta are constants set at alpha = 0.25 kcal/mol and beta = -0.005 kcal/mol. fi is the volume of ligand atom i, calculated from the amber radius of the ligand atom. For the receptor, these can be precalculated and stored on a grid. øDES,BULK(xi) and øDES,EXPL(xi) are interpolated from grids calculated using the solvgrid program during docking. It requires the calculation of two separate grids:<br />
<br />
blk_exp_dsol_grd<br />
<br />
where j is a rigid receptor atom, and Sj and fj are the solvent affinity and the fragmental volume of the receptor atom respectively. Bulk and explicit desolvation grids are calculated from fj and Sj at grid points p, distance rjp from the receptor atom multiplied by gaussian weighting of the distance. The solvgrid program calculates these grids from the charge and the volume of the receptor atoms.<br />
<br />
USAGE: solvgrid<br />
<br />
INPUT<br />
<br />
This programs require that an INRDSL file be created in the working directory, which contains the parameters to control the program. The INRDSL parameters for solvgrid are detailed below:<br />
<br />
receptor.pdb ; receptor pdb file<br />
parameters/ prot.table.ambcrg.ambH ; charge parameter file<br />
parameters/ vdw.parms.amb.mindock ; VDW parameter file<br />
box.pdb ; box pdb file<br />
0.33 ; grid spacing in angstroms<br />
1 ; es type: distance-dependent dielectric; 2: constant dielectric<br />
4 ; es scale for ff scoring<br />
2.3 2.8 ; bumping distances for polar and non-polar receptor atoms<br />
output_prefix ; output grid prefix name<br />
sol_op ; method for calculating desolvation grid<br />
solE_recep; solvation free energy of receptor<br />
<br />
OUTPUT FILES<br />
<br />
* OUTRDSL #restatement of input parameters; messages pertaining to calculation of the grids<br />
* OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file<br />
* PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file<br />
* output_prefix.bmp #bump grid<br />
* output_prefix.vdw #vdw values for receptor<br />
* output_prefix.es #electrostatic values for receptor<br />
* output_prefix.dsl #bulk and explicit desolvation grid for receptor</div>
JohnIrwin