AMBER Archive (2009)

Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Aug 11 2009 - 06:54:43 CDT

On Tue, Aug 11, 2009, Catein Catherine wrote:
>
> I can get implicit solvent system done without error message. However,
> for the TIP3P system, I can only finish the without nm calculation
> analysis. Everytime I do the nm calculation for the TIP3P system,
> following error message appears.

It's not clear what you are trying to do here...nmode cannot deal with
explicit solvent, periodic systems.
>
> /amber8/exe/nmode -O -i nmode_com.in -o nmode_com.1.out -c
> sanmin_com.1.restrt -p ../cpt_ser_complex2.prmtop not running properly

You need to carefully study the input and output files for this nmode
calculation. The "not running properly" is just a message from the wrapper
perl script. To track down the actual errors, you need to look at
nmode_com.1.out.

>
> I know previous users has also face the same problems, it seems to
> related to bugs in MM-GBSA, however, since the implicit solvent system
> can be done, it suspect it is due to other unknow reasons. Could anyone
> help?

There are all kinds of MM-PBSA related questions on the list, but many are
actually different problems. I'm uncertain about what you mean when you say
"the implicit solvent system can be done." Anyway, check the nmode.out file.

....dac

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