My sincerest apologies, nothing was wrong except for a missing space in the
command line. Sorry to waste anyone's time.
Duh!
On Wed, Nov 20, 2013 at 10:38 AM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
> Sorry, I forgot to say that I am using ambertools 13.
>
>
> On Wed, Nov 20, 2013 at 10:34 AM, Milo Westler <milo.nmrfam.wisc.edu>wrote:
>
>> Hi,
>> I've been trying to use ante-MMPBSA to create complex, receptor, and
>> ligand from a solvated protein-DNA complex topology file that I have used
>> in MD simulations.
>>
>> My input is:
>> ante-MMPBSA.py -p prmtop -c complex -r receptor -l ligand -s
>> ':Na+,:WAT'-n ':1-84'
>>
>> The ligand mask, -n ':1-84', represents the protein. Residues 85-108 are
>> the DNA and prmtop is a topology file that I have successfully used for the
>> MD.
>>
>> With this input I get:
>> Error: Unknown command-line arguments: :1-84
>>
>> If I only strip the Na+ and WAT, the program runs successfully.
>>
>> What am I doing wrong?
>>
>> --
>> -- Milo
>> ===================================================
>> National Magnetic Resonance Facility at Madison
>> An NIH-Supported Resource Center
>>
>> W. Milo Westler, Ph.D.
>>
>> NMRFAM Director
>> Senior Scientist
>> and
>> Adjunct Professor
>> Department of Biochemistry
>> University of Wisconsin-Madison
>> 433 Babcock Drive
>> Madison, WI USA 53706-1544
>> EMAIL: milo.nmrfam.wisc.edu
>> PHONE: (608)-263-9599
>> FAX: (608)-263-1722
>> =======================================================================
>> ========
>>
>
>
>
> --
> -- Milo
> ===================================================
> National Magnetic Resonance Facility at Madison
> An NIH-Supported Resource Center
>
> W. Milo Westler, Ph.D.
>
> NMRFAM Director
> Senior Scientist
> and
> Adjunct Professor
> Department of Biochemistry
> University of Wisconsin-Madison
> 433 Babcock Drive
> Madison, WI USA 53706-1544
> EMAIL: milo.nmrfam.wisc.edu
> PHONE: (608)-263-9599
> FAX: (608)-263-1722
> =======================================================================
> ========
>
--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
=======================================================================
========
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Received on Wed Nov 20 2013 - 09:00:04 PST
