[gmx-users] selecting res CYS from G53a5 using pdb2gmx

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Jan 9 01:25:25 CET 2013

I had modified three files: aminoacids.rtp, aminoacids.hdb and
residuetypes.dat. All these modifications were done prior running pdb2gmx.
So, I will be glad if you could let me know what the problem is.


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 5:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

On 1/8/13 6:58 PM, Payman Pirzadeh wrote:
> Hi,
> Found my solution; made an index file which had the protein and CYA in 
> the same group.
> Thanks for all your helps Justin.

I'm glad you found a solution, but for the purpose of being thorough I need
to say that this should not be necessary.  A residue listed as "Protein" in
residuetypes.dat, if added prior to running pdb2gmx, should lead to seamless
integration in the topology when running all subsequent steps in preparing
the system.  It is unclear to me what's going on here.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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