Re: [AMBER] issues

From: David Poole <>
Date: Fri, 22 May 2015 17:11:08 -0700

Thanks for your help. I've been using those parameters for other work but
found it likely better to build my own from the ground up. As noted in the
paper they mention the MTK approach as 'the recommended way of producing
the next generation heme parameters' (paraphrase).

I intended to take that advice as part of my work to produce a number of
ligated heme parameters to study some systems my group is interested in.

I am still having issues with the script properly reading input files.
I have two residues in a single pdb file, HEM for the porphyrin and FE2 for
the iron core. These both have mol2 files with the same residue names.

However, now when I run with this it claims that HEM is not found within
the naa mol2 file, which is quite frustrating nonsense.

-David Poole
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Received on Fri May 22 2015 - 17:30:03 PDT
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