[gmx-users] force field: heme group

[Justin A. Lemkul]

Matthew L. Danielson wrote:
> Ramachndran,
> 
> 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
> 

This sort of thing would make a nice addition to the "User Contributions" on the 
Gromacs site, if you're willing to make them widely available to the public :)

-Justin

> -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
>>>     
>>
>>   
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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