[gmx-users] How to create top of small molecules with pdb2gmx
tingguang.sun at gxust.edu.cn
Thu Mar 28 14:46:29 CET 2019
Thank you, Justin！
You mean that I should use the following command: "gmx pdb2gmx -f formic-acid.pdb -ter "？
I had used the flag -ter, but the program did not prompt interactive selection.
From: Justin Lemkul <jalemkul at vt.edu>
Date: 2019-03-28 21:16:22
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] How to create top of small molecules with pdb2gmx>
>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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