AMBER Archive (2009)

Subject: Re: [AMBER] Disulfide bond

From: Dong Xu (quantum_mania_at_yahoo.com)
Date: Tue Apr 21 2009 - 21:41:02 CDT

Thanks for the info. I looked up the AmberTools manual, it says "sleap addions won’t give the identical result as of tleap does due to the different set of vdw radii they are using." Is it still the case?

I'm a bit concerned about the radii. Can sleap set default PBradii mbondi2 or bondi or mbondi ? If so, will they be the same as tleap?

 Dong Xu
UC, San Diego

________________________________
From: Wei Zhang <zgjzweig_at_gmail.com>
To: Dong Xu <quantum_mania_at_yahoo.com>; AMBER Mailing List <amber_at_ambermd.org>
Sent: Tuesday, April 21, 2009 6:46:19 PM
Subject: Re: [AMBER] Disulfide bond

Hi,

      Sleap has the functionality to create disulfide bond automatically.
You can enable this function by add:

    set default disulfide auto

to your leaprc.

    What sleap does is it calculates the distance between two sulfur atoms
if the distance < disulfcut, a disulfide bond will be created and the residue
name will be changed accordingly.

   About the value "disulfcut", by default it is 2.1. it can be changed by

    set default disulfcut x.xx

   There is an example showing how to do this in directory:

    amber10/test/sleap/disulfide/Run.auto.H

    Sincerely,

    Wei

On Apr 21, 2009, at 8:37 PM, Dong Xu wrote:

> Hi,
>
> Is there a way to automatically identify the CYX residues and bond them in Leap?
>
> I found that sometimes it takes numerous trials to locate the correct CYX residue number for leap when there are additions in PDB files. It'd be nice to have a smart and automated way of doing that.
>
> Thanks!
>
> Dong Xu
> UC, San Diego
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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