AMBER Archive (2009)

Subject: Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates?

From: Paul Ledbetter (
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
in judgebondtype() of antechamber.c properly, exit

On Tue, Sep 15, 2009 at 17:12, case <> 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?
> ...dac
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