[gmx-users] heme

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 25 00:41:07 CET 2010

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


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