Re: [AMBER] mmpbsa with rigid bonds ?

From: Bill Miller III <>
Date: Mon, 15 Nov 2010 09:14:41 -0500

Use the same input file you have here (after removing ntc=2) and use the command line as you normally would, except place the -make-mdins
flag at the end of the command line. This will create all necessary mdin
files that will be used during the calculation, without actually running the
calculation. Then go into the newly created mdin files (named
_MMPBSA_*.mdin) using your favorite text editor and add ntc=2 to the &cntrl
section of those mdin files. Finally, use the same command from earlier to
execute, except place the -use-mdins flag in place of the
-make-mdins flag. This will tell to use mdin files that have
already been created (and modified) as they are instead of having them made
again by Note, do not change the names of the respective mdin
files because will only read in the mdin files with the names it
has already assigned to them. This also gives a lot more flexibility to the
user, but is also more prone to user errors that will not be caught by So take caution when using these flags with,

Good luck!


On Mon, Nov 15, 2010 at 9:01 AM, Jose Borreguero <>wrote:

> Dear Amber users,
> I'm having trouble using MMPBSA on a simulation that was carried out with
> rigid bonds involving hydrogens. The Van der Waals computed energy by
> is out of scale. I though of including the 'ntc=2' option in the following
> file:
> *&general
> endframe=2525, verbose=1,
> entropy=0,
> ntc=2,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100, fillratio=2.0, scale=1.0
> /*
> Unfortunately, the option 'ntc=3' is not understood by the parser. Does
> anyone has an idea of how can I call for rigid bonds in MMPBSA ?
> Best regards,
> Jose M. Borreguero
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Nov 15 2010 - 06:30:03 PST
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