Hai,
I am having the trouble to obtain the topology file while
attaching the prosthetic group to the target protein.Heme
ion is surrounded by the three aminoacids
HIS243,ASP185,HIS183 which all are within 3 A'
distance.While I am using the G43a1 force filed ,the error
is obtained as "Residue 'FE' not found in residue
topology database".On referring the files FFG43a1,ions in
"C:\cygwin\usr\local\gromacs\share\gromacs\top" we found
the presence of FE with the mass details. On trying to get
the top file from the DUNDEE PRODRG server ,I faced the
error as too many atoms in this molecule.It will be more
worthful if i come to know how to tackle this problem or
possible way to obtain the .top file information in any
other specific databases.
Thanking You.
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