AMBER Archive (2009)

Subject: [AMBER] Pentavalent Phosphorous and Antechamber

From: Peterson, Matthew W. (mpeterson_at_mitre.org)
Date: Wed Jun 03 2009 - 09:12:44 CDT

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
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