[gmx-users] energy minimization
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.
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.
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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