Erik Marklund wrote:
shahid nayeem skrev 2010-11-24 18.02:
Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds
with specbond.dat by pdb2gmx. After using editconf and genbox, when I
tried grompp I got error about unrecognized bonds/angles. I made bond
with MET SD and FE of Heme. As earlier suggested on this list I wrote
to get parameter for these bonds but I couldnt get it. If someone on
this mailing list can help me I will be grateful. Cyt C is very widely
modelled protein with Gomacs in literature hence I expect to get some
help from the forum.
shahid nayeem
A long time ago I simulated CytC with one of the gromos force fields. It
worked right out of the box. What forcefield are you using?
The same problem is frequently reported. The inter-residue bonds and angles are
not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence
the fatal errors. Perhaps something has changed since "a long time ago," but I
am sure problems exist in recent versions.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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