I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there. Shahid Nayeem
On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul <[email protected]> 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 > > -- > ======================================== > > 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 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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