[gmx-users] How to create top of small molecules with pdb2gmx

Justin Lemkul jalemkul at vt.edu
Thu Mar 28 14:16:33 CET 2019

On 3/28/19 9:15 AM, Tingguang.S wrote:
> Dear all,
>        I am trying to create the topology of a system with 100 formic acid molecules in the box. Charmm36 force filed was used, and I noticed that the corresponding entry for formic acid in this force filed was residue FORH. When I typed the command line: gmx pdb2gmx -f formic-acid.pdb, the error code is: "Atom HN in residue FORH 1 was not found in rtp entry FORH with 5 atoms". It seems that pdb2gmx automatically added the N terminus. How can I avoid this auto addition of the terminus. If pdb2gmx can not be used to generate a small molecule top file, then how can I make use of the parameters which had been defined in the existed force filed files (In this case, the residue FORH).

Interactively select terminal patching and choose "None"



Justin A. Lemkul, Ph.D.
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