msnayeem at gmail.com
Thu Nov 25 05:23:47 CET 2010
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but
Met SD and FE bond is not there.
On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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