AMBER Archive (2008)

Subject: AMBER: reg unstability of structure in md

From: balaji nagarajan (
Date: Wed Dec 03 2008 - 22:17:51 CST

dear amber ,
I am a new user to amber ,
I changed my pdb format and loaded in xleap its loaded ..,
and i am sure my pdb is quite in a right form isn't it .,
it gave a message in terminal like this ...

dna1 = loadpdb "j0.pdb"
Loading PDB file: ./j0.pdb
  total atoms in file: 808
  Leap added 448 missing atoms according to residue templates:
       448 H / lone pairs

I solvated the structure in water (TIP3P)
by giving

solvateoct model2 TIP3PBOX 8.0

and i viewed the pdb its good

but when i do the minimization and the procedure as given in poly-AT tutorial
in explicit water for 120 ps ..
my molecule is no more stable it went bad
what could be the reason
help me out to solve the problem
thanks in advance .....

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