Dear Art, Thanks a lot for the reference. Regards, Sarada >> Message: 5 > Date: Fri, 12 Dec 2008 19:21:02 -0800 > From: Arthur Roberts <[email protected]> > Subject: Re: [gmx-users] [Fwd: Loss of bonds in HEME iron after > pdb2gmx] > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Dear Sarada, > > You need to paramterize the Cysteinyl ligand manually. There are a > variety of references in the literature that provide reasonable > energies. Below is a pretty good reference. > > Best wishes, > Art > > 1. Oda, A., Yamaotsu, N., and Hirono, S. (2005) New AMBER force field > parameters of heme iron for cytochrome P450s determined by quantum > chemical calculations of simplified models, J. Comput. Chem. 26, > 818-826. > > > On Dec 9, 2008, at 10:59 PM, [email protected] wrote: > >> Hello, >> I am working with the simulation of cytochromeP450. There is a bond >> between the S of cystine and FE of HEME. During the grompp step I get >> warnings that there is no default bonds/angles/dihedrals all >> pertaining to >> the cystine-heme bond. In the archives it was mentioned that these >> values >> must be taken from ffG**bon.itp and included in the topology file. >> However >> in the ffG**bon.itp file, the bonds/angles mentioned seem to be >> between S >> of CYS and the carbon atom of HEME. For eg, >> >> ; bond-, angle- and dihedraltypes for specbonds: >> [ bondtypes ] >> S S 2 gb_33 >> NR FE 2 gb_32 >> ; cystine - heme link (is CR1-S, use CH2-S): >> S CR1 2 gb_30 >> >> Should not the cystine - heme link have FE insteadof CR1? I understand >> that I am missing some crucial point here. Kindly help. >> Thanks. >> Sarada >> Graduate student, >> NCBS, >> Bangalore
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