Re: [AMBER] mmGBSA and solute dielectric constant

From: Jason Swails <>
Date: Thu, 4 Jul 2013 17:09:44 -0400

On Thu, Jul 4, 2013 at 11:19 AM, Changqing Yan <>wrote:

> Hi Jason,
> I think I can get your meaning but I cannot put it into practice. Since
> when I run again, a new _MMPBSA_gb.mdin file was generated and inside there
> are no longer the term which I add. would you lease specify how I can
> achieve what you mean?
> My input file was:
> Input file for running PB and GB&general endframe=2000,interval=40,
> keep_files=0, receptor_mask=:1-682:688-694,
> ligand_mask=:683-687,verbose=2, strip_mask=:WAT:Na+, use_sander=1,/&gb
> igb=5,/
> and my script to run is
> pbs_mpirun $AMBERHOME/bin/ -O -i -o
> mmpbsaigb5e4md2-3.dat -sp ...
> .
> My procedure is to run the script, and then Cntrl+C when the
> _MMPBSA_gb.mdin was formed. And I changed the
> _MMPBSA_gb.mdin file and then run the script again.

This is not necessary. If you add the flag -make-mdins to's
command-line, then it will quit immediately after making the input files
for each program. In order to actually use the mdin files you just
created, you need to add the "-use-mdins" flag to the
command-line. Without this flag, will just create new input


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Jul 04 2013 - 14:30:02 PDT
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