AMBER Archive (2009)

Subject: [AMBER] COOH group troubling

From: Jio M (jiomm_at_yahoo.com)
Date: Sun Dec 06 2009 - 07:57:06 CST

Dear AMBER users;

I have a docked ligand which has COOH group.

When I do minimisation, there are stars ****** in mdout. So I checked
for overlapping atoms.I obtained rst file from small steps minimisation
before getting stars ***** (as suggested to my previous mails) and got
the pdb. I found that O oxygen of C=O and O oxygen of C-OH are making
bond with each other.

After removing extra bond in xleap manually I saved it as  inpcrd
and  prmtop file.  I had  to give box information in
inpcrd file. Again in minimisation same atoms are overlapping or making
bonds. I am using frcmod file also for ligand. Is there any parameter
getting missed.

Please reply

thanks and regards;

JIomm

      
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