[gmx-users] HB3 ATOM
jalemkul at vt.edu
Mon Sep 3 20:25:29 CEST 2018
On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote:
> Yes. Now my problem is HG in residue CYS that I don't know rename to what!!!
Either the names in the PDB file need to be made consistent with what is
in the .rtp file, or you should use -ignh to have pdb2gmx ignore all
input H atoms and build its own, all of which will be properly named.
> On Mon, 3 Sep 2018 22:49 Justin Lemkul, <jalemkul at vt.edu> wrote:
>> On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote:
>>> my pdb file named HB2 and HB3 but .rtp file in my force field named
>>> HB2. and so on error "atom HB3 in residue xxx was not found in rtp entry"
>>> can I rename HB2 to HB1 and HB3 to HB2 ?
>>> or any idea?!
>> Have you tried it?
>> Justin A. Lemkul, Ph.D.
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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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