AMBER Archive (2009)

Subject: Re: [AMBER] Disulfide bond

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Tue Apr 21 2009 - 22:30:36 CDT

Hi,

    This is not the case now. Now addions will give identical result
as tleap does.

    Sleap set same PBradii as tleap does. By default it uses MBONDI.
it can also use
bondi or mbondi2, you just need to

     set default PBradii bondi (or mbondi2)

     Sincerely,

     Wei

On Apr 21, 2009, at 9:41 PM, Dong Xu wrote:

> 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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