AMBER Archive (2009)

Subject: Re: [AMBER] error in MM PBSA

From: Hemant Gangwar (hemant_at_physics.iisc.ernet.in)
Date: Sat Apr 04 2009 - 12:08:08 CDT

   it seems because of some reason velocity of some atom has increased a
lot,may be it is because of very low mass.
> Dear amber
> i am using MM PBSA...while save .prm & .inpcrd files for a co-crystallised
> PDB file it showed error that the atom types of Chloreine atoms in the
> ligand were undefined. so i deleted those atoms from the PDB and then i
> could continue.
>  Then i went on to run min.in and heat.in file...the heat.out file showed
> that   
>     "vlimit exceeded for step 28 and vmax =......
> ......
>  
>    c o-ordinate resetting(SHAKE) can't be accomplished, deviation too  
> large.
> NITER< NIT, LL, I and J are 0, 1884, 3737, 3339
>  Note: this usuaaly is a symptom of some deeper problem with energetics of
> the system  "
>  
> help?
>
>
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-- 
Hemant Gangwar
Graduate Student
Centre for Condensed Matter Theory
Indian Institute of Science
Bangalore
Mob-9632726167
www.physics.iisc.ernet.in/~hemant

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