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