[gmx-users] Adding residue to .rtp file
raji.phy at gmail.com
Wed Oct 24 20:46:46 CEST 2018
Thank you for your reply. I have few more questions
1. Yes, command pdb2gmx continued and generated the topology. The warning
is about 74 atoms which are from the new added rtp entry. I just want to
understand more about the warning. I dont find any related information?
2. What is the significance of the atom types in the rtp file?
CTL3 - carbon of methyl group
CG331 - Aliphatic C for methyl group
What is the difference between them and How to choose the right one for
carbon in alkyl chain?
> Message: 1
> Date: Fri, 19 Oct 2018 18:32:23 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Adding residue to .rtp file
> Message-ID: <eb75936f-47a3-ce9b-cf0e-2059ee843e4c at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> On 10/18/18 11:45 AM, Raji wrote:
> > Hi,
> > I have added the modified residue entry in the rtp file and able to
> > generate to topology and .gro file. but i got this warning when passing
> > pdb2gmx command.What is this about?
> > "WARNING: there were 74 atoms with zero occupancy and 0 atoms with
> > occupancy unequal to one (out of 160 atoms). Check your pdb
> That warning should not present a problem and pdb2gmx should continue.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 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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