[gmx-users] energy minimization

Smith, Micholas D. smithmd at ornl.gov
Wed Jul 25 14:49:29 CEST 2018

LigParGen generates new atom types for each ligand topology it generates. The output files from LigParGen should contain terms for opls800-925 (if necessary) in the generated topology file. These need to be included in the force-field file you use for use in your simulations. 

A warning should be made about LigParGen: each atom is given a unique atomtype. For instance if you have a 25 atom ligand, you will have atomtypes opls 800 through opls824. Some of these may be repeats. This means that if you want to run with a different ligand you have to change these atomtype definitions each time.

Hope that helps.

Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Wednesday, July 25, 2018 8:17 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] energy minimization

On 7/24/18 7:24 AM, farial tavakoli wrote:
> Dear Justin
> I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file.
>   when I issued this command:
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor
> faced this error:ERROR 1 [file LIG.itp, line 11]:
>    Atomtype opls_800 not found
> I checked the aminoacids.rtp file  of  /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype opls_800 and 801 and ... in this file. while the LIG.itp which generated by LigParGen server has atomtype opls_800 , 801 and ... .
> I have to modify all of these atomtype opls_ in order to correspond to with aminoacid.rtp file?
> I would be thankfull if you help me.
> bestFraial

It looks like your topology introduces new atom types. Check the
LigParGen documentation to see if it requires a different version of the
force field or if the parameters are provided somewhere.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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