[AMBER] COOH group troubling

From: Jio M <jiomm.yahoo.com>
Date: Sun, 6 Dec 2009 05:57:06 -0800 (PST)

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;


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Received on Sun Dec 06 2009 - 06:00:05 PST
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