msnayeem at gmail.com
Fri Nov 26 12:02:27 CET 2010
I am using ffG43a1 force field. It has heme topology. But in Cyt C. FE is
bonded to both NR of HIS and SD of MET. The parameter for the bond, FE SD,
angles e.g. NR (HIS) FE SD(MET) and dihedral angle CH2(MET) SD (MET) FE
NR(HIS) is missing in this force field. hence I am getting error while
running grompp. Please suggest me what should I do.
On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund <erikm at xray.bmc.uu.se> 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?
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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