AMBER Archive (2009)

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

From: Catein Catherine (
Date: Wed Aug 12 2009 - 21:23:40 CDT

Dear Prof. Case,


I should have described the situation better. Sorry.


I have done the simulation with explicit and implicit solvents. Then, I extract the snapshots from the mdcrd files and do the MM-GBSA analysis for both systems.


If I do the MM-GBSA, without nmode calculation. Both calculations can be finished without error.


If I do the MM-GBSA, with nmode calculation, only the snapshots from implicit solvent calculations can be done.


I used no-solvent prmtop files for all the calculations. I set BOX=YES to extract snapshots from explicit solvent mdcrd files. Atttached is the nmode.out file for the calculation with error, at the end of the file, I found:



Total memory required : 1604498119 real words


Total memory required : 60129519 real words


Maximum nonbond pairs: 59399549

ASSERTion 'ier ==0' failed in nmode.f at line 105.



What should I do to solve this problem?


Best regards & thanks,




> Date: Tue, 11 Aug 2009 07:54:43 -0400
> From:
> To:
> Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
> 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 -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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