Dear Francois,
the fragment that I have sent contains only the residue for which I would like to get the GAFF atom types and the charges, but of course I ran Antechamber on a tripeptide, thus capping the open valences. The fragment is part of a glycopeptide containing unusual amino acids and linkers, so want to try to model it in GAFF as well as in the macromolecular AMBER forcefield (02). Thank you for the links, I think it will take time to go through them.
best,
Krisztina
--------------------------------------------
On Fri, 6/21/13, FyD <fyd.q4md-forcefieldtools.org> wrote:
Subject: Re: [AMBER] GAFF atom type for CO
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Friday, June 21, 2013, 8:49 AM
Dear Krisztina,
Do you want to perform atom typing for a molecular
fragment?
For sure Antechamber will generate errors for the atoms with
an open
valency...
R.E.D. Python performs atom typing for whole molecules as
well as
their molecular fragments. I will send you a link for
demonstration;
(frcmod & leaprc files are also generated).
So now, I think your best bet is to build a _dipeptide_ i.e.
cap this
fragment with the ACE & NME chemical groups. Then,
derive the charges
and build the force field library(ies) for the central
fragment (and
may be the N-term & C-term fragments):
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
& may be
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
You could do that in global approach with R.E.D. Server:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
and even all automatically from your dipeptide:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27
Here a limitation in R.E.D. Server is that a computation
is
re-executed if a new input is generated; thus, in the global
approach
a given input is generated several times; with R.E.D. Python
this will
be far more efficient as the inputs are compared before
execution, and
not re-ran if found identical.
Once you got the force field libraries generated by R.E.D.
and/or
R.E.D. Server (mol2 file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php)
(or mol3 with
R.E.D. Python
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
with the connecting atoms defined) you can manually define
the atom
types (using a script; See for instance the 'F-93' R.E.DD.B.
project
and its LEaP script:
http://q4md-forcefieldtools.org/REDDB/projects/F-93/).
Last point: do you plan to incorporate this fragment in a
protein
(from what I understand from the PDB file you sent)? this
means you
need to use a FF for proteins (FF99SB? FF03?) and not
GAFF...
regards, Francois
> 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 and tried both sqm from
version 12 and
> divcon from version 9, with sqm being worse
(assigned
> "c1"). I tried "-j
5" option and used -nc 1 for
> the charge. Is there any way to force an atom type or
what is it
> dependent on?
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Received on Fri Jun 21 2013 - 03:00:02 PDT
