[gmx-users] pdb2gmx, charmm22 and HEME

[Erik Marklund]

Dear users,

I am trying to preprocess a cytochrome C structure with pdb2gmx and have run into some problems. The forcefield has parameters for the HEME group, but other components are missing to successfully produce the topology etc. First of all, the hdb files don't have an entry for HEME, but I managed to make one myself (which I am happy to share with the gromacs community). What's worse however, is that the histidine that sits bang on top of the Fe in the HEME is turned into a HIS1, which isn't found in the ftp files:

...
Linking CYS-14 SG-109 and HEM-105 CAB-845...
Linking CYS-17 SG-129 and HEM-105 CAC-853...
Linking HIS-18 NE2-139 and HEM-105 FE-866...
Linking MET-80 SD-626 and HEM-105 FE-866...

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Program pdb2gmx, VERSION 4.6.6-dev-20131203-a2e1958-unknown
Source code file: /u/jlpb/marklund/src/gmx/release-4-6/gromacs/src/kernel/resall.c, line: 642

Fatal error:
Residue 'HIS1' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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How do I resolve this issue? This has been discussed in the mailing list before, but so far I've only found dead ends

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ