Dear Aparna,
You have to again cross check the input structure of ligand.
Such as Bond orders and atom types.
For example Valency of Carbon should be 4 not more or less than it.
likewise you have to check it.
All the Best
On Fri, Feb 22, 2013 at 4:37 PM, Aparna P <aparnaspap.gmail.com> wrote:
> Hi
>
> I am a research scholar working in computational Physics.while I was
> preparing the prep and frcmod files an error occurred which I have pasted
> below.
> I dont know how to how to tackle the problem.I double checked the input
> structure but I couldnt find any error.
> Will u please help me?
>
> This is the error message
>
> 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 "/opt/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
> Aparna.P
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>
--
*Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228*
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Received on Fri Feb 22 2013 - 03:30:03 PST
