[gmx-users] Loss of bonds in HEME iron after pdb2gmx

saradas at ncbs.res.in saradas at ncbs.res.in
Tue Nov 25 10:50:01 CET 2008

I am working with the simulation of cytochromeP450. In the output of the
pdb2gmx command, the iron atom in the HEME loses all the bonds, including
the sulphide bond with cystine. Also, the command changed the residue name
from HEME to HEC. During the execution of the pdb2gmx, I get this warning:

Warning: 'HEC' not found in residue topology database, trying to use 'HEME'

Can someone please tell me, if this is responsible for the loss of bonds
especially the one between CYS and FE. How can the bonds be retained?

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