Hi Soong,
Just a quick comment: it looks like you want MMPBSA calculation?
However, if you put the igb=2 flag, the calculation is MM-GBSA.
HTH,
Pin-Chih
On Wed, Nov 11, 2015 at 8:12 AM, Soong Jiaxin <jiaxinsoong.gmail.com> wrote:
> 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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> >
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--
Pin-Chih Su Ph.D.
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
900 South Ashland Avenue, Room 1052
Chicago, IL 60607-7173
office 312-996-5388
fax 312-413-9303
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Received on Sat Nov 14 2015 - 13:30:05 PST
