[gmx-users] energy minimization

[Justin Lemkul]

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