On Mon, 2014-02-24 at 11:31 +0000, almarques wrote:
> Hi,
>
> I have bee trying to run the mmpbsa.py for alanine scanning mutagenesis
> but I always get this error:
>
> Loading and checking parameter files for compatibility...
> PrmtopError: Couldn't predict mask from topology files!
> Your ligand residues must be sequential in your complex.
> There are likely problems with your topology files if this is not the
> case.
>
> My input is:
>
> sample input file for running alanine scanning
> &general
> startframe=3000, endframe=5000, interval=1000,
> verbose=1,
> ligand_mask=':1-200,806,810',
> receptor_mask=':201-401,402-603,604-805,807,808,809,811,812,813',
Consider simplifying your receptor mask to ':201-805,807-809,811-813'
Also, it would help to know what version of AmberTools you are using.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 24 2014 - 05:30:05 PST
