AMBER Archive (2009)

Subject: Re: [AMBER] S-S problem-in protein

From: Rilei Yu (
Date: Mon Oct 12 2009 - 01:28:14 CDT

Dear Dr. Jason,

Thanks for your very detailed suggestion, and I will have a try!


Rilei Yu

--- 09年10月12日,周一, Jason Swails <> 写道:

发件人: Jason Swails <>
主题: Re: [AMBER] S-S problem-in protein
收件人: "AMBER Mailing List" <>
日期: 2009年10月12日,周一,下午12:24

After reading a little about leap and sleap commands in the ambertools
manual, the automation of disulfide bond creation appears to be unique to
sleap.  You can turn automatic disulfide bond creation to 'off', 'auto', or
'manu'.  If you set it to off, it will not create disulfide bonds.  If you
set it to 'auto', (which I believe is default) it will create disulfide
bonds between two sulfurs on CYX residues if they fall within 'disulfcut'
angstroms of one another.  Disulfcut is a variable you can define that has a
default value of 2.2 angstroms.  If set to 'manu', it'll ask you before
creating the bonds.  There may be some way of automating this in tleap or
xleap using bondByDistance, but I would suggest trying out sleap.  Look at
the commands "disulfide" and "disulfcut" in the ambertools manual (which can
be found quite easily by either googling or perusing for
more information if you need it.
All the best,

2009/10/11 Jason Swails <>

> Rilei,
> Leap adds hydrogens by default according to a template in all_amino94.lib,
> which is designed to make the process of creating topology files from PDBs
> easy.  However, this makes the different protonation states of various
> residues slightly more complex (i.e. different protonation states of
> Histidine, Aspartate, Glutamate, etc.). Thus, each protonation state is
> given its own residue name.  Cysteine, too, can either be a free residue
> capped by a hydrogen, or it can be involved in a disulfide bond with another
> cysteine (yielding a cystine).  Thus, a free cysteine has the 3-letter code
> CYS, but each cysteine member of a cystine (cysteine dimer) has the 3-letter
> code CYX according to all_amino94.lib.  Therefore, if you wish to change
> your cysteines into cystines, change each CYS in the pdb into CYX.
> In this detail, I may be mistaken, so somebody please correct me if I am, I
> am drawing from recollection of my own experiences adding S-S bonds.  If you
> are using tleap or xleap, you will have to manually add the S-S bonds
> (either through the 'bond' command detailed in the ambertools manual, or by
> hand in xleap if that's possible, I've never tried that approach).  However,
> if you use sleap, I believe that it adds the disulfide bonds for you.
> Hope this helps,
> Jason
> 2009/10/11 Rilei Yu <>
> Dear amber users,
>> When i load my protein that contains 7 S-S,I found the these disufides
>> bonds were all open, and one hydrogen is linked to the "S"-atom terminal, so
>> I edit them in the xleap one by one, it is really time consuming, because I
>> will edit many such complex! Do anyone know is there any better approach to
>> solve this problem?
>> Thanks for your help!
>> Rilei Yu
>>      ___________________________________________________________
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> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list

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