I don't think you need to make any changes in APS.DAT. You need to make
changes in your pdb file as antechamber accept (probably residue name or
atom type or initial numbering) . I was getting the same error.
Shubhra
On Wed, Jun 3, 2009 at 7:12 PM, Peterson, Matthew W. <mpeterson.mitre.org>wrote:
> Hello,
>
> We are trying to run MD on a transition state, which contains a pentavalent
> phosphorous. When we run antechamber to parameterize the ligand, we're
> getting the following error:
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
>
> Error: cannot run "/Users/mpeterson/sw/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
> I'm guessing the correct action here is to adjust the valence penalty
> parameters in APS.DAT, but I've looked at the file and I'm unsure of how to
> do this. Does anyone have any experience with this?
>
> Thank You,
>
> Matt
>
> Matthew Peterson
> The MITRE corporation
> mpeterson (at) mitre (dot) org
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> Email Scanned for Virus & Dangerous Content by : www.CleanMailGateway.com
>
>
>
--
Shubhra Gupta
Information Officer,
Department of Bioinformatics & Structural Biology
Indian Institute of Advanced Research
Koba Village
Gandhinagar 382007 Gujarat
Phone: 91-79-30514154
Email: shubhg.iiar.res.in
Home Page: http://www.guptalab.org/shubhg/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 04 2009 - 01:15:34 PDT
