Error in minimization and MD...

From: Mausumi Mazumdar <>
Date: Mon 9 Oct 2000 11:13:03 +0530 (IST)

Dear sir,
       I am facing two major problems in dealing with my present system

1) While performing minimization for a decapeptide system with some
  new residues built like AIB, there is a constant error that the
structure is not being minimized as after nearly 300000000 runs also the
energy is very high.

2) And with that energy while trying to perform MD in vaccum it is giving
an error " Coordinates resetting cannot be done as the deviation is too
large". Firstly i thought that it must be due to improper minimization but
taking a couple of standard amino acid residue also it gave the same

  Till now i am not able to figure out the mistake.Is it possible that
such errors occur due to some parameter described in the FRCMOD file.

   Sir it will be very kind of u if u can throw some light on this.

Thanking you in advance.

Mausumi Mazumdar
Reasearch Student
Indian Institute of Science
Received on Sun Oct 08 2000 - 22:43:03 PDT
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