AMBER Archive (2009)

Subject: Re: [AMBER] COOH group troubling

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Dec 06 2009 - 09:05:07 CST

It would probably help us out if you included the frcmod that you're using
so we don't have to guess at what's going on, along with your mol2 or prep
file for the custom ligand.

Good luck!
Jason

On Sun, Dec 6, 2009 at 8:57 AM, Jio M <jiomm_at_yahoo.com> wrote:

> 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
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber