AMBER Archive (2005)

Subject: Re: AMBER: Force field modification problem

From: David A. Case (case_at_scripps.edu)
Date: Mon May 30 2005 - 11:21:00 CDT

On Mon, May 30, 2005, yuann wrote:

> I've noticed one strange problem when I tried to replace
> the current force field parameters. I'd like to simulate a
> RNA(single strand)-ligand complex, and I defined only a new atom
> type called OT(as OH behaves) on O3' in the tail of my single
> strand RNA ribose in order to reproduce, such as OH-CT-CT-OH
> defined in parm98. This is because my ligand(mainly carbohydrates)
> contains many OH and I prefer to use Glycam force field on my ligand.
>
> However, I can't obtain the same 'RNA_only' topology file after such
> modification(AMBER8/tleap). Thanks in advance for your help.

I am not sure what you mean here: what exactly is the problem you have?
I don't understand that phrase "the same ... topology file": same as what?

...regards...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu