[AMBER] COOH group:extra undesired bond

From: Jio M <jiomm.yahoo.com>
Date: Tue, 6 Apr 2010 21:09:31 -0700 (PDT)

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....




--- 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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Received on Tue Apr 06 2010 - 21:30:04 PDT
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