# Difference between revisions of "AMSOL"

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AMSOL is a semiempirical quantum chemistry program that includes the MINDO/3, MNDO, AM1, and PM3 gas-phase Hamiltonians, the CM1A, CM1P, CM2/AM1, CM2/PM3, CM3/AM1, and CM3/PM3 charge models for calculating partial atomic charges, the SM1 - SM5.42R solvation models for calculating free energies of solvation in water, the SM4 solvation model for calculating free energies of solvation in alkanes, and the SM5.42R, SM5.4, SM5.2R, and SM5.0R solvation models for calculating free energies of solvation in any organic solvent. Most of the solvation models are based on the AM1 and/or PM3 Hamiltonians; the SM5.2R model is also available with the MNDO Hamiltonian. AMSOL can also accept user-specified specific reaction parameters. All solvation models that are denoted with an "R" in their name are for rigid-solute calculations and were designed to utilize accurate gas-phase geometries to predict solvation free energies. For all other models, geometry optimization is possible in both the gas phase and solution. For SM5.4 models analytic derivatives are available for geometry optimization. | AMSOL is a semiempirical quantum chemistry program that includes the MINDO/3, MNDO, AM1, and PM3 gas-phase Hamiltonians, the CM1A, CM1P, CM2/AM1, CM2/PM3, CM3/AM1, and CM3/PM3 charge models for calculating partial atomic charges, the SM1 - SM5.42R solvation models for calculating free energies of solvation in water, the SM4 solvation model for calculating free energies of solvation in alkanes, and the SM5.42R, SM5.4, SM5.2R, and SM5.0R solvation models for calculating free energies of solvation in any organic solvent. Most of the solvation models are based on the AM1 and/or PM3 Hamiltonians; the SM5.2R model is also available with the MNDO Hamiltonian. AMSOL can also accept user-specified specific reaction parameters. All solvation models that are denoted with an "R" in their name are for rigid-solute calculations and were designed to utilize accurate gas-phase geometries to predict solvation free energies. For all other models, geometry optimization is possible in both the gas phase and solution. For SM5.4 models analytic derivatives are available for geometry optimization. | ||

− | * AMSOL is used by [[ZINC]] and | + | * AMSOL is used by [[ZINC]]. |

+ | |||

+ | ==Installation== | ||

+ | Go here: https://secure.nouvant.com/umn/technology/z05201/license/153/agreements/new | ||

+ | Install this on sgehead: ~]# | ||

+ | yum install compat-gcc-34-g77.x86_64 | ||

+ | Fill in the license information. <br /> | ||

+ | Download the gzip file.<br /> | ||

+ | Unzip it.<br /> | ||

+ | Change into the directory and run the amsol.compile file.<br /> | ||

+ | |||

+ | == Compiling == | ||

+ | If you're on a newer Linux machine and get errors compiling, then you may need to apply the following changes to '''new/amsol.f''': | ||

+ | <pre> | ||

+ | 26,27c26,27 | ||

+ | < OPEN(19,NAME='fort.19') BJL1003 | ||

+ | < OPEN(20,NAME='fort.20') BJL1003 | ||

+ | --- | ||

+ | > OPEN(19,file='fort.19') BJL1003 | ||

+ | > OPEN(20,file='fort.20') BJL1003 | ||

+ | </pre> | ||

+ | |||

+ | If you don't know what that means, then just find the file '''new/amsol.f''' and find lines 26 and 27 which should be | ||

+ | OPEN(19,NAME='fort.19') BJL1003 | ||

+ | OPEN(20,NAME='fort.20') BJL1003 | ||

+ | and replace that with | ||

+ | OPEN(19,file='fort.19') BJL1003 | ||

+ | OPEN(20,file='fort.20') BJL1003 | ||

+ | |||

+ | ===Patches=== | ||

+ | For using Amsol7.1 with dock3.7, we distribute a patch: | ||

+ | $DOCKBASE/ligand/amsol/patches/amsol7.1_port_intcar.f.diff | ||

+ | |||

+ | This patch resolve an issue with linear molecules. | ||

+ | |||

+ | Consider applying this patch and then recompile amsol7.1. | ||

+ | <pre> | ||

+ | patch port/intcar.f ${DOCKBASE}/ligand/amsol/patches/amsol7.1_port_intcar.f.diff | ||

+ | </pre> | ||

+ | |||

+ | ===Large Molecules=== | ||

+ | By default AMSOL limits the number of heavy atoms to 60 and the number of light atoms (i.e. hydrogens) to 60. To increase the limit, | ||

+ | in '''include/SIZES.i''' edit the following line | ||

+ | |||

+ | PARAMETER (MAXHEV=60, MAXLIT=60, NCHAIN=60, NRELAX=25) DL0397 | ||

+ | |||

+ | to, for example, | ||

+ | |||

+ | PARAMETER (MAXHEV=80, MAXLIT=110, NCHAIN=60, NRELAX=25) DL0397 | ||

+ | |||

+ | and recompile by running make in the base directory | ||

+ | |||

+ | make | ||

+ | |||

+ | |||

+ | |||

− | |||

[[Category:Solvation]] | [[Category:Solvation]] | ||

− | [[Category: | + | [[Category:Software]] |

+ | [[Category:Freecom]] |

## Latest revision as of 13:56, 30 October 2021

From the AMSOL Web Site:

AMSOL is a semiempirical quantum chemistry program that includes the MINDO/3, MNDO, AM1, and PM3 gas-phase Hamiltonians, the CM1A, CM1P, CM2/AM1, CM2/PM3, CM3/AM1, and CM3/PM3 charge models for calculating partial atomic charges, the SM1 - SM5.42R solvation models for calculating free energies of solvation in water, the SM4 solvation model for calculating free energies of solvation in alkanes, and the SM5.42R, SM5.4, SM5.2R, and SM5.0R solvation models for calculating free energies of solvation in any organic solvent. Most of the solvation models are based on the AM1 and/or PM3 Hamiltonians; the SM5.2R model is also available with the MNDO Hamiltonian. AMSOL can also accept user-specified specific reaction parameters. All solvation models that are denoted with an "R" in their name are for rigid-solute calculations and were designed to utilize accurate gas-phase geometries to predict solvation free energies. For all other models, geometry optimization is possible in both the gas phase and solution. For SM5.4 models analytic derivatives are available for geometry optimization.

- AMSOL is used by ZINC.

## Installation

Go here: https://secure.nouvant.com/umn/technology/z05201/license/153/agreements/new Install this on sgehead: ~]#

yum install compat-gcc-34-g77.x86_64

Fill in the license information.

Download the gzip file.

Unzip it.

Change into the directory and run the amsol.compile file.

## Compiling

If you're on a newer Linux machine and get errors compiling, then you may need to apply the following changes to **new/amsol.f**:

26,27c26,27 < OPEN(19,NAME='fort.19') BJL1003 < OPEN(20,NAME='fort.20') BJL1003 --- > OPEN(19,file='fort.19') BJL1003 > OPEN(20,file='fort.20') BJL1003

If you don't know what that means, then just find the file **new/amsol.f** and find lines 26 and 27 which should be

OPEN(19,NAME='fort.19') BJL1003 OPEN(20,NAME='fort.20') BJL1003

and replace that with

OPEN(19,file='fort.19') BJL1003 OPEN(20,file='fort.20') BJL1003

### Patches

For using Amsol7.1 with dock3.7, we distribute a patch:

$DOCKBASE/ligand/amsol/patches/amsol7.1_port_intcar.f.diff

This patch resolve an issue with linear molecules.

Consider applying this patch and then recompile amsol7.1.

patch port/intcar.f ${DOCKBASE}/ligand/amsol/patches/amsol7.1_port_intcar.f.diff

### Large Molecules

By default AMSOL limits the number of heavy atoms to 60 and the number of light atoms (i.e. hydrogens) to 60. To increase the limit,
in **include/SIZES.i** edit the following line

PARAMETER (MAXHEV=60, MAXLIT=60, NCHAIN=60, NRELAX=25) DL0397

to, for example,

PARAMETER (MAXHEV=80, MAXLIT=110, NCHAIN=60, NRELAX=25) DL0397

and recompile by running make in the base directory

make