[gmx-users] heme

Erik Marklund erikm at xray.bmc.uu.se
Wed Nov 24 22:42:53 CET 2010


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?

-- 
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/




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