[gmx-users] re : heme group

sanjay23 at iitb.ac.in sanjay23 at iitb.ac.in
Sat Jan 10 06:55:04 CET 2009

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.


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