[gmx-users] selecting res CYS from G53a5 using pdb2gmx
jalemkul at vt.edu
Wed Jan 9 01:04:29 CET 2013
On 1/8/13 6:58 PM, Payman Pirzadeh wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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