[gmx-users] re : heme group

[sanjay23 at iitb.ac.in]

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