AMBER Archive (2008)

Subject: Re: AMBER: [amber/glycam] dealing with fucose...

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Thu Jul 10 2008 - 07:59:34 CDT

Hi Lachele,

First of all thanks a lot for a quick reply. I really do appreciate that. It was terribly needed and useful. Thanks once again. The post was really very helpful.

What I have done now is that I have downloaded the glycam06 parameter and prep files from http://www.glycam.com/gl_params.html as you mentioned. After that I have renamed fucose to 1fA, and galactoses to 1LB and ZLB respectively in the pdb file, according to the naming convention on the website. (http://www.glycam.com/CCRC/biombuilder/biomb_index.jsp)

Right now, the problem that I have is that the residue ZLB (2,3 Beta D Galactose) has the hydrogen atom at position 1, where I have the oxygen in the pdb file. This causes xleap to flag a couple of errors when I try to save the top and crd files. Xleap adds the missing oxygens when I load the pdb file.

Here is the output from xleap on loading pdb file:
------------------------------------------------------------------------------------------------------------------
 Added missing heavy atom: .R<CGLY 530>.A<OXT 8>
Created a new atom named: O1 within residue: .R<ZLB 532>
  Added missing heavy atom: .R<ZLB 532>.A<O2 19>
  Added missing heavy atom: .R<1LB 533>.A<O1 1>
  Added missing heavy atom: .R<CGLY 1076>.A<OXT 8>
Created a new atom named: O1 within residue: .R<ZLB 1078>
  Added missing heavy atom: .R<ZLB 1078>.A<O2 19>
  Added missing heavy atom: .R<1LB 1079>.A<O1 1>
  total atoms in file: 5306
  Leap added 5582 missing atoms according to residue templates:
       6 Heavy
       5576 H / lone pairs
  The file contained 2 atoms not in residue templates

----------------------------------------------------------------------------------------------------------------

And, here is the output from xleap when I try to save the top and crd files:

----------------------------------------------------------------------------------------------------------------
Checking Unit.
ERROR: The unperturbed charge of the unit: -15.164000 is not integral.
WARNING: The unperturbed charge of the unit: -15.164000 is not zero.
FATAL:  Atom .R<ZLB 532>.A<O1 21> does not have a type.
FATAL:  Atom .R<ZLB 1078>.A<O1 21> does not have a type.
Failed to generate parameters
Parameter file was not saved.
----------------------------------------------------------------------------------------------------------------

I would be very thanful to you if you could respond to this and help me out.
Waiting for you response,
Thanks,

Kind regards,
Waqas.

----- Original Message ----
From: Lachele Foley (Lists) <lf.list_at_gmail.com>
To: amber_at_scripps.edu
Sent: Tuesday, July 8, 2008 7:08:52 PM
Subject: Re: AMBER: [amber/glycam] dealing with fucose...

Hi Waqas,

Before we get off onto a lengthy discussion...  You -did- mean 1FA and
not F1A, right?  The proper name for the residue is 1FA.

Also, did you try using our builder online to make your complex?  Did
you have problems with it?  You might find that to be a much easier
way to go.  If something didn't work, let us know.  We have a mailing
list you can join when you register.  Or send email to
glycam_at_gmail.com if you prefer.

Also, why do you want a frcmod file?  If I understand you correctly,
you shouldn't need it for this.  The parameter and prep files should
be all you need (for fucose, that is).  You can download the latest
versions of the Glycam parameters here:

http://www.glycam.com/gl_params.html

You
 want Glycam_06.prep and Glycam_06d.dat.  For linking to proteins,
you also need the glycam_amino* libraries.  The leaprc.Glycam06 might
also be useful to you.

:-) Lachele

On 7/8/08, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
>
>
>
>
>
> Hi,
>
> Hope every thing is working fine at your side.
>
> Well, I am a new user of glycam and amber, just a couple of weeks old, and I am trying to do some studies with protein carbohydrate complex.
>
> The complex that I have contains beta-d-galactose and alpha-l-fucose with the protein chain (The trisaccharide resides in the binding pocket of the protein and is not covalently attached to it).
>
> With 2 galactoses one can rename them in the pdb file as 1GB and ZGB (since one galactose has linkage position
 1, and the other one has linkage positions 2 and 3) but with fucose I am a bit confused because its not present in the standard glycam04 forcefield. I thought of building that  residue with "biomolecule builder"  (http://www.glycam.com/CCRC/biombuilder/biomb_index.jsp) but could not find a way to generate the prep & frcmod files for F1A  (alpha-l-fucose with linkage position 1) residue that I need. I tried antechamber as well but there I do have some missing parameters.
>
> What I am trying to do now is to find a way to generate the prep and frcmod files for this resiue in order to make it recognized in amber, so that I could rename this residue in pdb file and then load the whole pdb (with protein and carbohydrate) to generate top and crd files.
>
> I appologize if my language is not that proper or clear. I hope
 that you did
 understand it. I request you to please let me know if I am on the right track or if there is some problem with my understanding of the subject matter.
>
> I would really appreciate if you could respond.
> Wish you and your team all the best!
>
> Thanks,
> Kind regards,
> Waqas.
>
>
> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
2-0263
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