I did provide the same MMPBSA.py input file when I ran the make-mdin file.
The _MMPBSA_gb.mdin is the resultant file. Do you mean that the correct
program to be used for this newly created _MMPBSA_gb.mdin file should be
sander instead of MMPBSA.py?
Regards,
Vanessa
On 11 Nov 2015 20:59, "Jason Swails" <jason.swails.gmail.com> wrote:
> On Wed, Nov 11, 2015 at 5:23 AM, Soong Jiaxin <jiaxinsoong.gmail.com>
> wrote:
>
> > Hi, my command line was:
> >
> > MMPBSA.py -O -i _MMPBSA_gb.mdin
>
>
> This is wrong. _MMPBSA_gb.mdin is a *sander* input file created by
> MMPBSA.py to run sander. It is not an MMPBSA.py input file, and attempts
> to use it as so will result in an error (since MMPBSA.py recognizes
> different input than sander does).
>
> -use-mdins simply means that _MMPBSA_gb.mdin must *exist* -- it will be
> used automatically. You still need to provide the same MMPBSA.py input
> file you used when you ran the -make-mdins file.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Nov 11 2015 - 05:30:07 PST
