On Mon, May 28, 2012, ashley chen wrote:
> But for residues with aspartic acid
> and glutamic acid it gives me the following error.
>
> 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
>
> when the follow antechamber command is used:
> antechamber -i mol.log –fi gout –o mol.mol2 –fo mol2 –c resp
For charged molecules, you must use the -nc flag to set the net charge on the
molecule. I'm guessing that this might be your problem.
Also, when you encounter problems, use the acdoctor program to look for
possible solutions.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 28 2012 - 06:30:02 PDT
