Re: AMBER: implicit minimization

From: David A. Case <>
Date: Fri, 28 Sep 2007 08:17:16 -0700

On Fri, Sep 28, 2007, Dr. Devanathan Raghunathan wrote:

> I have a problem using sander amber9. When I am simulating explicit
> solvent systems, it works, but if I try to change the parameter to
> implicit solvents (just changed 1 parameter), the calculation is crashed
> with the following error :

Was there anything the the output file?

> This is my minimization file
> Minimization with Cartesian restraints
> &cntrl
> imin=1, maxcyc=200,
> cut=300, igb=7, saltcon=0.2, gbsa=1,
> intdiel=1.0, extdiel=78.5,
> ntpr=10, ntx=1, ntb=0,
> ntr=1
> /
> Just changing the igb=7 to igb=0 and removing ntb=0 from the input file
> allows the calculation to proceed.
> thanks for your insights...

Note that you changed *two* things: the default in Amber is ntb=1, so the
run that worked was using periodic boundary conditions, and the one that
failed was not. Is your system supposed to be periodic or not? Implicit
solvent simulations are never periodic, explicit simulations usually are.
Setting a value for ntb that doesn't match the prmtop file will lead to
problems, and Amber might not be smart enough to notice the inconsistency.


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Received on Sun Sep 30 2007 - 06:07:41 PDT
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