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