Ok, I understand it now. I have mistakenly thought that I should use
_MMPBSA_gb.mdin
as the input file in the command line.
Thank you very much for your help.
Regards,
Vanessa
On 11 November 2015 at 21:27, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Nov 11, 2015 at 8:18 AM, Soong Jiaxin <jiaxinsoong.gmail.com>
> wrote:
>
> > I did provide the same MMPBSA.py input file when I ran the make-mdin
> file.
> >
>
> No you did not. You said your command was
>
> MMPBSA.py -i _MMPBSA_gb.mdin ... -use-mdins
>
> In this case, you provided _MMPBSA_gb.mdin as the input file. This file
> should not have existed when you ran MMPBSA.py with the -make-mdins flag.
> If you do
>
> MMPBSA.py -i mmpbsa.in ... -make-mdins
>
> then your next command, after editing the _MMPBSA_gb.mdin file as you need
> to, should be
>
> MMPBSA.py -i mmpbsa.in ... -use-mdins
>
> 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?
> >
>
> M
> MPBSA.py will call sander automatically. If you specify -use-mdins, then
> MMPBSA.py will *not* create its own _MMPBSA_gb.mdin file and instead will
> use the one that already exists.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Nov 11 2015 - 06:30:04 PST
