[gmx-users] Re: pdb2gmx error

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 27 19:55:18 CEST 2012

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


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