[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?

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/

More information about the gromacs.org_gmx-users mailing list