AMBER Archive (2009)

Subject: Re: [AMBER] Disulfide bond

From: quantum_mania_at_yahoo.com
Date: Wed Apr 22 2009 - 00:25:45 CDT

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
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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