AMBER Archive (2009)

Subject: Re: [AMBER] Disulfide bond

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Wed Apr 22 2009 - 10:00:02 CDT

Hi Dong,

    I think the output is correct. My understanding of the CONECT is:

    (1) each disulfide bond will be reported by two CONECT card: for
both ending atoms

    (2) each CONECT card describe connections of one sulfur atom.

   Thus,

     CONECT 139 136 4979

   means atom 139 (10.SG) has two bonds: on with atom 136 (10.CB), the
other with 4979(335.SG).

    Meanwhile, another CONECT card was printed for atom 4979 as

    CONECT 4979 139 4976

    which basically describe the disulfide bond again.

     Sincerely,

     Wei

On Apr 22, 2009, at 12:25 AM, quantum_mania_at_yahoo.com wrote:

> Thanks, Wei. I just tried sleap in AmberTools and it looked like the
> automatic disulfide bonding was working, see below
>
> [gtkleap]$ rec=loadpdb myprotein.pdb
> make bond between atom 136 4975
> make bond between atom 636 708
> make bond between atom 1533 2246
> make bond between atom 2266 2324
> make bond between atom 2959 3130
> make bond between atom 2980 3104
> make bond between atom 3556 3770
> make bond between atom 5042 5443
>
> Then I opened the amber PDB file output from sleap using "savepdb".
> At the end of the amber PDB file, there were CONECT records:
>
> CONECT 139 136 4979
> CONECT 639 636 711
> CONECT 711 639 708
> CONECT 1536 1533 2249
> CONECT 2249 1536 2246
> CONECT 2269 2266 2327
> CONECT 2327 2269 2324
> CONECT 2962 2959 3133
> CONECT 2983 2980 3107
> CONECT 3107 2983 3104
> CONECT 3133 2962 3130
> CONECT 3559 3556 3773
> CONECT 3773 3559 3770
> CONECT 4979 139 4976
> CONECT 5046 5043 5447
> CONECT 5447 5046 5444
>
> Here's how I bonded disulfide bonds in tleap using residue number.SG:
> bond rec.10.SG rec.335.SG
> bond rec.42.SG rec.47.SG
> bond rec.102.SG rec.149.SG
> bond rec.151.SG rec.156.SG
> bond rec.197.SG rec.210.SG
> bond rec.199.SG rec.208.SG
> bond rec.236.SG rec.253.SG
> bond rec.339.SG rec.364.SG
>
> Now I'd like to know how sLeap and CONECT record work. Use the 1st
> disulfide bond as an example:
>
> tLeap: bond rec.10.SG rec.335.SG
>
> sLeap: make bond between atom 136 4975
>
> CONECT record: CONECT 139 136 4979
>
> These atoms are: atom 136=residue 10.CB atom 4975=residue 335.HA
> atom 139=residue 10.SG atom 4979 = residue 335.SG
>
> My questions are:
>
> 1. Why sleap reported bonding between other atoms than SG in these
> CYX residues?
> 2. How do CONECT records work? There are 8 disulfide bonds, but 16
> CONECT records. I don't how they are constructed.
>
> Thanks!
>
>
> 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 8:30:36 PM
> Subject: Re: [AMBER] Disulfide bond
>
> 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
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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>
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