AMBER Archive (2009)
Subject: Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates?
From: Paul Ledbetter (pjl1_at_rice.edu)
Date: Tue Sep 15 2009 - 18:34:54 CDT
No, the program does not continue to run after that. I have never
seen antechamber run after that warning, so I thought that warning was
enough to imply that it crashed.
The rest of the warning is:
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 "/users/pjl1/local/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full"
in judgebondtype() of antechamber.c properly, exit
On Tue, Sep 15, 2009 at 17:12, case <case_at_biomaps.rutgers.edu> wrote:
> On Tue, Sep 15, 2009, Paul Ledbetter wrote:
>> I have an AMBER prep file in cartesian coordinates which I'd like to
>> convert to internal coordinates. I had to do a bunch of hand editing
>> of the final prep file in cartesian coordinates, so I'd like to avoid
>> doing things over from the pdb and ac files.
>> antechamber -i pca-pB.prepc -fi prepc -o pca-pB.prepi -fo prepi
>> and got a "Warning: the assigned bond types may be wrong, please :"
>> I don't want any bonds reassigned, so I did:
> Prep files don't contain any bond type information (this is not used by
> Amber), so I don't see the danger here. Does the program continue to run,
> after the warning?
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