[gmx-users] re : heme group

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jan 10 11:38:56 CET 2009

Well, if you look into the .rtp files for the GROMOS force field,
you'll find heme in there, but maybe not in the right form or not in
the format you have in the .pdb file. Whether something is in the
residue (building block) topology libaray is not prinicply related to
being amino acid. As if the computer would care for the distinction.
You can't use John's approach for heme, using prodrg in that way, as
it is covalently bound to the protein. You'll have to add bonds,
angles, dihedrals, etc manually, which is not recommended unless you
know what you're doing. pdb2gmx can handle such coupling automatically
through a file listing special bonds between building blocks, as in
the .rtp file.
The archives contain lots of info on all these topics.



On Sat, Jan 10, 2009 at 6:55 AM,  <sanjay23 at iitb.ac.in> wrote:
> hi,
> heme group is not an amino acid, pdb2gmx only support the amino acids
> because .itp and .dat file in gromacs have only information about protein
> atoms not for other. so u just cut the co-ordinate of heme group from your
> pdb file save it in other pdb file and give input for Prodrg software it
> will return u co-ordinate of heme group in gromacs compatible format. u do
> pdb2gmx on only protein part and add both output file(pdb2gmx.gro and
> prodrg .gro)and proceed next step. u should read online John E. Kerrigan
> GROMACS Tutorial for Drug – Enzyme Complex. it will help u more.
> http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
> sanjay
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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