[gmx-users] force field: heme group

Matthew L. Danielson mldaniel at purdue.edu
Wed Nov 11 23:30:23 CET 2009


If you are trying to use the AMBER force field ports for Gromacs 
(assuming you installed them correctly), I have defined the HEME group 
for Amber03.   If this would help you let me know, and i can provide the 
files that you need to replace in your gromacs "top" folder

-Matt Danielson-
Justin A. Lemkul wrote:
> Ramachandran G wrote:
>> Dear all,
>>        It is known that force field for the heme group doesn't exist
>> in gromacs. So i tried to use amber force fields(AMBER94, AMBER99,
> That's not true; all of the Gromos variants have heme parameters.
>> AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest
>> gromacs version 4.0.5 but still it gives the error message
>> 'Residue 'HEME' not found in residue topology database'
>> Can anyone help me how to solve this problem. Thanks for your help.
> Well, what is it that you tried?  The error message is quite clear - you do not 
> have a [ HEME ] directive in the .rtp file for whatever force field you're 
> trying to use.
> -Justin
>> Rama


Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
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West Lafayette, IN 47907-2091

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