Dear David,
I attached the tripeptide. I built it in Accelrys Discovery Studio Visualiser 3.5 and afterwards I cleaned geometry - whatever that means there. I tried the raw built strucutre too. I understand that the charges are independent of the atom types, but I wanted to simulate my molecules in GAFF too, because they are deviating from amino acids too much. I run the follwoings:
antechamber -i igc-dap+-dal_dsv.pdb \
-fi pdb \
-o igc-dap+_dal_dsv.mol2 \
-fo mol2 \
-c bcc \
-s 2 \
-j 5 \
-nc 1
In my experince the version 12 Antechamber is rejecting a lot molecules than the version 9.
Thank you,
Krisztina
--------------------------------------------
On Thu, 6/20/13, David A Case <case.biomaps.rutgers.edu> wrote:
Subject: Re: [AMBER] GAFF atom type for CO
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Thursday, June 20, 2013, 10:55 PM
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 Fri Jun 21 2013 - 02:00:02 PDT
