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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phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
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