[gmx-users] energy minimization

Justin Lemkul jalemkul at vt.edu
Wed Jul 25 14:17:27 CEST 2018

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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