Dear gmx-users,
I am new to Gromacs and trying to simulate a protein with a heme group using
CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running
pdb2gmx .
WARNING: atom HA is missing in residue HEM 513 in the pdb file
You might need to add atom HA to the hydrogen database of building
block HEME
in the file aminoacids.hdb (see the manual)
WARNING: atom HB is missing in residue HEM 513 in the pdb file
You might need to add atom HB to the hydrogen database of building
block HEME
in the file aminoacids.hdb (see the manual)
WARNING: atom HC is missing in residue HEM 513 in the pdb file
You might need to add atom HC to the hydrogen database of building
block HEME
in the file aminoacids.hdb (see the manual)
.
.
.
.
.
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449
Fatal error:
There were 30 missing atoms in molecule Protein, if you want to use this
incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Can anyone help how can I generate and add hydrogen database information for
heme to be used with CHARMM27 ff?
Thanks,
Sundar Jubilant
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