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

Justin Lemkul jalemkul at vt.edu
Wed Jan 9 01:04:29 CET 2013

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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