On 6/27/12 1:52 PM, shounakb wrote:
Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?
Justin, could this be an issue?
Please see the previous posts on these topics, including the post from just a
few minutes ago where I discovered the source of the problem. The FOR residue
issue has been an ongoing discussion over several weeks. I will maintain that I
do not necessarily believe that a two-atom model of a formyl group is
sufficiently accurate for a Gromos force field, since the alpha proton is very
polar and thus may need to be explicitly represented. I have stated my
skepticism before but it appears Shima is pursuing the current course. Side note ;)
-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
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