AMBER Archive (2009)

Subject: [AMBER] antechamber bond type error

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Fri Dec 18 2009 - 16:26:57 CST

Hi, I am trying to parameterize a molecule (protonated, positively charged retinal) and I am getting the following error when I put in the following input:

[bgs0244_at_opt-login01 makelibdir]$ antechamber -i rt.log -fi gout -nc 1 -o rt.prep -fo prepc -c resp -s 2

Running: /usr/local/amber/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

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 MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/usr/local/amber/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit

I get three files as output,
ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_BOND_TYPE.AC0 ATOMTYPE.INF

I am not sure how to read the first two, but i checked the connectivity in ATOMTYPE.INF, and it looked fine.
I don't think I can recompile anything because I am using AMBER on a public computing environment.
I don't know where to find APS.DAT or in which direction to change the valence penalty parameters, or if I am allowed to do it, even.

Are there any suggestions? I read one of the emails that said that molecules that can be described by multiple resonance structures may be problematic in antechamber. Could this be the source of a fatal error for me or something?

Thanks,
Mark
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