[gmx-users] energy minimization

[Smith, Micholas D.]

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

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

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