Dear Amber Users,
I want to simulate an iron-amino acid complex. I have derived the charges using
standalone RED perl codes. To generate the topology files I am following the
given tutorial (
http://ambermd.org/tutorials/advanced/tutorial1_adv/).
However, I am stuck in the frcmod generation part. On running xleap it suggests
that some bond and angle parameters related to Fe are missing. I have two
options:
1. using parmchk (however, for some reasons I am not able to generate a mol2
file using tleap. It gives me a syntax error. On creating mol2 file using babel,
parmchk fails to work as the atom names are different.
2. to identify the bond and angle parameters from the X-ray structure. Would
this method be accurate ??
I cannot use antechamber as it does not deal with metals.
Is there any other way of generating the frcmod files ???
Regards
Soma
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Received on Fri Nov 18 2011 - 10:00:06 PST
