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.gmail.com>
To: amber.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.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.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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Received on Sun Jul 13 2008 - 06:07:27 PDT
