[gmx-users] Re: generating a top file

Yang Ye leafyoung at yahoo.com
Sun Jun 10 16:59:46 CEST 2007

Hi, Saf

We use a special bond for heme, specified in specbond.dat. Check the 
mailing list archive.

Yang Ye

On 6/10/2007 9:17 PM, Shahrokh Safarian wrote:
> Dear Yang YE
> Thank you very much for your kind cooperation. I did upload my pdb file
> to prodrg but there were two problems:
> 1) the size of the file was high
> 2) there was an Fe atom which was not supported by prodrg
> In fact I am trying to simulate an iron containing enzyme which dose not
> contained of a typical heme group. So, as you know, if we want to have a
> good simulation, the Fe3+ ion should be covalently bounded to the
> nitrogen atoms of at least two or three His residues until the ion has
> not been moved from its initial location in the molecule. Did hoy have
> any similar experience before and could you lead me to solve this
> problem?
> Thanks
> saf

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