Hi,
I think I solved the problem of the previous antechamber run: what probably caused the problem, is that the hydroxyl group, which was not attached to teh rest, actually belonged to a 2nd and 3rd residue. I corrected that, but I still got some problem: H atoms in the two methylene group are not recognised and are assigned to a DU atom type. Could someone tell me why?
Thanks in advance,
Krisztina
--- On Wed, 11/7/12, Krisztina Feher <feher_krisztina.yahoo.com> wrote:
From: Krisztina Feher <feher_krisztina.yahoo.com>
Subject: Re: [AMBER] bond missing in phosphate group after antechamber run
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Wednesday, November 7, 2012, 10:55 PM
Sorry, I forgot to attach the antechamber output files, here they are.
Krisztina
--- On Wed, 11/7/12, Krisztina Feher <feher_krisztina.yahoo.com> wrote:
From: Krisztina Feher <feher_krisztina.yahoo.com>
Subject: [AMBER] bond missing in phosphate group after antechamber run
To: amber.ambermd.org
Date: Wednesday, November 7, 2012, 8:00 PM
Hi,
I am trying to derive GAFF parameters for a modified DNA residue with antechamber. I capped the residue with H's and ran through antechamber and parmcheck without error. However the bond between the oxigen and phosphorus is missing in the mol2 file as well as the respective parameters in the .frcmod file. Could someone have a look at teh input pdb file for antechamber to figure out the reason for this?
Thanks in advance,
Krisztina
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Received on Thu Nov 08 2012 - 05:30:02 PST
