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 (askamber23_at_hotmail.com)
Date: Thu Aug 13 2009 - 22:38:02 CDT

Dear Prof. Case,

 

The explict and implict calculations were did for two different models (with different size). So, it may be the reason why I can got the implict calculations done without error message. If I still want to do the analysis for model calculated with explict solvent, what is the proper way to solve the problem? I set BOX=YES when I extract snapshots from the mdcrd files. Does it stripped out all waters too? I used the prmtop of ligand, receptor and complex without solvent. But since the MD was run with explicit solvent, what is the proper way to stripp out all waters for MM-GBSA calculations?

 

Pls kindly instruct.

 

Best regards,

 

Cat.
 
> Date: Thu, 13 Aug 2009 07:46:02 -0400
> From: case_at_biomaps.rutgers.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
>
> On Thu, Aug 13, 2009, Catein Catherine wrote:
> >
> > Total memory required : 1604498119 real words
> > Total memory required : 60129519 real words
> > ASSERTion 'ier ==0' failed in nmode.f at line 105.
>
> You are asking for 1.6 billion words, or 13 Gbytes of memory, and the
> assertion is telling you that you don't have that much memory available.
>
> Have you stripped out all the waters? Or is there some other reason why the
> snapshots from the explicit simulation have more atoms than those from the
> implicit solvent simulation? (The two systems should be the same size, and
> you say that the implicit solvent system worked.)
>
> ...dac
>
>
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