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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
