Hi Krisztina,
Your emails are a bit unclear. What exactly you having problems with and what exactly are your questions? In your original email you asked "Is there any way to force an atom type or what is it dependent on?" Francois gave advice for this using R.E.D. For antechamber, by specifying the "-at" flag, you can force the atom typing to be specific for your desired force field; if you don't specify this then it defaults to gaff atom types (see AmberTools12 manual). Plus, you can manually edit the file and replace the atom types with those you want at anytime you want. (Atom types are defined at the beginning of the parameter files located in your local $AMBERHOME/dat/leap/parm directory.) But beware of this route because you might introduce atom type combinations that will result in many missing parameters.
If you are having problems with computing partial atomic charges, then take a look again at Francois's email. If you want to use divcon via antechamber to compute charges, then make sure that your input structure is a good one (ie. proper bond lengths and angles). If divcon interprets the input structure with "broken" or "not present" covalent bonds when they should be present then it will have trouble. As mentioned before, divcon charges and gaff atom types will not be ideally balanced with the parm99SB or Glycam, while R.E.D. is designed to do exactly this.
Cheers,
Karl
----- Original Message -----
From: "Krisztina Feher" <feher_krisztina.yahoo.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Friday, June 21, 2013 10:59:41 AM
Subject: Re: [AMBER] GAFF atom type for CO
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 - 03:30:02 PDT
