Dear Sir,
>>See if there are differences between those parameters and yours.
I have attached two files comparing COOH parameters--ff99SB of ASH
(ASH_cooh) and COOH parameters-GAFF of my molecule (my_cooh). There are
some differences. But if I see force constants in my_cooh file they
seem to be more rigid (higher values) compared to ASH_cooh. Should I or
Can I use parameters of ASH_cooh in my_cooh..
please suggest
>...good luck....
thanks
regards,
JIomm
--- On Sat, 4/3/10, case <case.biomaps.rutgers.edu> wrote:
From: case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] COOH group:extra undesired bond::NO reply :-(
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Saturday, April 3, 2010, 2:31 PM
On Fri, Apr 02, 2010, Jio M wrote:
>
> I had same problem before also, subject being: "COOH group troubling"
>
> Now I have different molecule, whose N is to be further attached to
> other residues and then minimisation. But the COOH is showing undesired
> bond while doing minimisation. The RESP charges were derived. The bond
> is between C of carbonyl and H of OH. So a sort of triangle being
> formed.
Take a look at the ASH and GLH residues in the Amber libraries (and their
corresponding force field parameters.) These are neutral carboxylic acids,
and have been used a lot in real simulations, without the problems you
mention. See if there are differences between those parameters and yours.
...good luck....dac
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- application/octet-stream attachment: ASH_cooh
- application/octet-stream attachment: my_cooh
Received on Sun Apr 04 2010 - 00:30:03 PDT
