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?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 21 2013 - 00:00:02 PDT
