On Thu, Jun 20, 2013, Krisztina Feher wrote:
>
> I would like to assign GAFF atom types to diamino-pimelic acid (DAP)
> with Antechamber (see attahced pdb file), but the carbonyl carbons
> both on the backbone and on the sidechain as assigned "c2"
> atom types instead of "c". I embedded DAP in a tripeptide to
> derive the atom types ...
Can you send the pdb file you used for the full tripeptide? You just had
the amino acid fragment in your earlier email, which means that we can
not easily be sure of reproducing what you did.
> ....and tried both sqm from version 12 and divcon
> from version 9, with sqm being worse (assigned "c1").
The assignemnt of atom types has nothing to do with which quantum program is
used to compute the AM1 charges.
...regards...dac
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Received on Thu Jun 20 2013 - 14:00:02 PDT
