[gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

[Justin Lemkul]

On 12/13/19 12:29 PM, Sadaf Rani wrote:
> Hi Alessandra
> I used it but top file extension is not supported. Should I give a combined
> PDB file? I got ligand topology from an external server when I will give
> combined PDB, it will give an error for not having these residues in the
> database.
>
> Could you please suggest which file should I give?
>
> Here is undermentioned command which I used for the -merge option.
>
> gmx pdb2gmx -f G6PD_topol.top -merge G6P_topol.top

If you want a merged topology, you need to write an .rtp entry for your 
ligand and not rely on a separate .itp file.

-Justin

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Justin A. Lemkul, Ph.D.
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