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

From: Waqas Nasir <>
Date: Fri, 11 Jul 2008 02:47:36 -0700 (PDT)

Hi Lachele,

Hope you are fine. Thanks again for the help that you have provided me with. It has really proved to be substantial.

Well, again as you mentioned I had a brief look at the tools manual and now I think I do understand your point quite clearly. What I have done now is that I have renamed 1fA to 0FA, 1LB to oLB (where oLB = sequence { ROH 0LB }) and ZLB to zLB (where zLB = sequence { ROH ZLB }) in the pdb file.

The oxygens are at the position where they are supposed to be. Every thing looks perfectly alright until I run the loadpdb command which results in the following error;
!FATAL ERROR----------------------------------------
!FATAL:    In file [chirality.c], line 121
!FATAL:    Message: Atom HO1 is not in the first list

I am extremely sorry for the trouble that I am causing you, but it seems every time there is something silly going on with me. Anyways, I will be very grateful to you if you could help me out this time as well.

Thanks alot for the assistance... it was all worthed.
Thanks again,
Stay blessed!

Kind Regards,

--- On Thu, 7/10/08, Lachele Foley (Lists) <> wrote:
From: Lachele Foley (Lists) <>
Subject: Re: AMBER: [amber/glycam] dealing with fucose...
Date: Thursday, July 10, 2008, 10:24 AM


Glad to be of help.

The first thing I see is that the residue ZLB should not contain an O1
atom at all, but it appears that it does. Perhaps the pdb file has an
O1 in its ZLB residue. It might be sufficient, for this problem, to
delete that atom from the file. It also appears that your ZLB does
not have an O2 atom because leap is trying to add one. It is probably
ok to let leap add that atom. I also suspect that your 1LB residues
should actually be named 0LB (this might also be the case for your
fucose residue). See the next paragraph, and then you can decide.

Here's a little more about our naming convention: As you know, when
the glycans link together, they lose an "HOH". Our residues are set
up so that the anomeric position loses the OH (except when anomeric
links to anomeric), and the non-anomeric position loses the H. All
residues (with a special exception, below) should be missing an oxygen
at their anomeric carbon. So, to get, for example, a complete,
normal, a-D-Glcp, you have to add an ROH (-OH residue, named ROH to
avoid confusion) to complete the molecule at the anomeric position.
The AmberTools manual has much more to say about this, and you might
find the information there helpful. The initial residue numbers tell
use where there are attachments in addition to the anomeric position.
So, for example, 3GB tells us that the b-D-Glcp has attachments at its
O3 as well as at the anomeric position. A residue that attaches only
at the anomeric position is numbered zero, e.g., 0GB. A plain
a-D-Galp molecule, therefore, in our naming convention, is ROH-0LA.
The special residue 1GB is used only when two anomeric posititions
attach to each other, e.g. 1GB-0GB, which is b-D-Glcp-1-1-b-D-Glcp
(1GB exists because one of them has to have an oxygen). Of course,
for some sugars, the anomeric carbon is not C1, and the names behave
accordingly. Note, in light of this, that your glycine must contain
the oxygen that forms the link between the protein and the glycan
(unless it doesn't link at the anomeric position). Leap appears to be
adding a linkage oxygen to the glycine. If you are attaching the ZLB
to the glycine at the ZLB's C1, deleting the O1 from the ZLB should
make things better.

Please see the AmberTools manual, section 3.5, for a much more
detailed discussion of this. I think it will answer many of your
questions -- and might clarify any confusion I caused in the last
paragraph. You will also find examples of leap input commands.

Let me know how it goes.

:-) Lachele

On 7/10/08, Waqas Nasir <> wrote:
> 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
> What I have done now is that I have downloaded the glycam06 parameter and
prep files from 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.
> 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
> 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
> Waiting for you response,
> Thanks,
> Kind regards,
> Waqas.
> ----- Original Message ----
> From: Lachele Foley (Lists) <>
> To:
> 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
> 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:
> 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 <> 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"
( 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
> 2-0263
> -----------------------------------------------------------------------
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:-) Lachele
Lachele Foley
The AMBER Mail Reflector
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To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

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Received on Sun Jul 13 2008 - 06:07:43 PDT
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