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 - 05:30:10 PST
