AMBER Archive (2009)

Subject: [AMBER] error in MM PBSA

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Sun Apr 05 2009 - 23:27:21 CDT

 
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  "
 
helpp?

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