On Aug 2, 2013, at 2:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Aug 2, 2013 at 11:39 AM, Hunter Brown <bassoongoon.earthlink.net> wrote:
>> Thanks for showing me that mask. I am still getting the error:
>>
>> SelectionError: Invalid selection! Integers expected.
>> Exiting. All files have been retained.
>>
>> Is this a problem with my script (selecting residues?) or something more concerning?
>
> I assumed that qm_residues would accept a mask expression, but looking
> at the manual that may not be the case:
>
> "qm_residues Comma- or semicolon-delimited list of complex residues to
> treat with quantum mechanics..."
>
> mmpbsa gurus may want to correct me here, but maybe you could try
>
> qm_residues='N-M'
>
> or
>
> qm_residues='N,M,O'
>
> where {N M O} are residue numbers.
This is correct. It does not take a mask, it takes a comma-delimited list of residues.
I may adjust it so that it recognizes masks, but when MMPBSA.py was originally written there was no available Python mask parser, which prevented me from accepting masks as input.
All the best,
Jason
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Sat Aug 03 2013 - 07:00:02 PDT
