From: David A Case <>
Date: Fri, 20 Dec 2013 13:41:17 -0500

On Fri, Dec 20, 2013, Arjun Sharma wrote:
> I am trying to generate mol2 file from pdb file of a polymer which is
> 120 atoms long but I keep bumping into this error message when I try to
> run antechamber
> 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

This almost always means that there is something wrong with the input
structure. Examine it visually to make sure that structure looks OK, all of
the hydrogens are present, etc. If you can't figure out what is going on, you
may have to post the input file you are using.


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Received on Fri Dec 20 2013 - 11:00:03 PST
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