<font color='black' size='2' face='arial'><font color="black" face="arial" size="2"><font face="Arial, Helvetica, sans-serif">Dear gmx-users,<br>
<br>
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 .<br>
<br>
WARNING: atom HA is missing in residue HEM 513 in the pdb file<br>
You might need to add atom HA to the hydrogen database of building block HEME<br>
in the file aminoacids.hdb (see the manual)<br>
<br>
<br>
WARNING: atom HB is missing in residue HEM 513 in the pdb file<br>
You might need to add atom HB to the hydrogen database of building block HEME<br>
in the file aminoacids.hdb (see the manual)<br>
<br>
<br>
WARNING: atom HC is missing in residue HEM 513 in the pdb file<br>
You might need to add atom HC to the hydrogen database of building block HEME<br>
in the file aminoacids.hdb (see the manual)<br>
<br>
.<br>
.<br>
.<br>
.<br>
.<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.3<br>
Source code file: pdb2top.c, line: 1449<br>
<br>
Fatal error:<br>
There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at http://www.gromacs.org/Documentation/Errors<br>
-------------------------------------------------------<br>
<br>
Can anyone help how can I generate and add hydrogen database information for heme to be used with CHARMM27 ff?<br>
<br>
Thanks,<br>
<br>
Sundar Jubilant<br>
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