AMBER Archive (2008)

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

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Tue Jul 15 2008 - 09:45:19 CDT

I've attached the modified pdb file. Leap complains about some of
your conect cards, but I assume those correspond to residues you
removed from the pdb file. Otherwise, it seems to load properly.

I loaded the modified pdb file into xleap in Amber 10 using the
following commands:

logfile nowat_log
source leaprc.GLYCAM_06
m1 = loadpdb sample_mod.pdb

To check that the molecules looked right, I issued the xleap command
"edit m1" and visually inspected the display.

The changes I made to the pdb were:

* Add TER cards between the separate glycan molecules (otherwise, leap
might try to connect them).
* Change GAL to 2LB and FUC to 0fA.
* Move the O1 in each GAL/2LB into a new residue positioned just
before the GAL/2LB residue.
* Rename the O1 residue to ROH.
* Ensure that each residue has a unique residue number.

Note that this procedure generates two complete a-L-Fucp-1-2-b-D_Galp
molecules that are not otherwise attached to any other residues or
molecules. If those are to be attached to a protein, further
modifications might be necessary. I can probably help with that if
you have problems.

Let me know if I may be of further assistance.

:-) Lachele

On Sat, Jul 12, 2008 at 3:44 PM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
>
> Hi,
>
> Thanks for the reply, and sorry for bothering you. The thing is that I just
> want to load the fucose and galactose residues in Xleap to get started. I am
> attaching a sample pdb file taken from 2vng.pdb which contains only
> carbohydrate residues FUC and GAL. If you could just load this into the
> xleap and tell me what steps have you taken to do so, it will be a great
> help. Please note that this pdb file also contains that O1 (oxygen at
> position 1) in GAL residue that means that you will have to manage it
> through ROH. One more thing that I want to tell you is that the case which I
> am dealing with is one of non bonded interaction of carbohydrate with
> protein making a complex.
>
> I thank you once again for your help. I feel that I am very close and
> hopefully it will be over in a couple of days.
>
> Awaiting your response,
> Kind regards,
> Waqas.
>
> ----- Original Message ----
> From: Lachele Foley (Lists) <lf.list_at_gmail.com>
> To: amber_at_scripps.edu
> Sent: Friday, July 11, 2008 5:19:17 PM
> Subject: Re: AMBER: [amber/glycam] dealing with fucose...
>
> What are you trying to build? Or, more specifically, what is it that
> your pdb file should represent?
>
> If your 0LB residue is connected to another glycan or to a protein,
> then you don't want an ROH in the file in a position associated with
> the 0LB. That will only confuse things. The same goes for your ZLB.
> If this is the case, you're going to put the other glycan (or protein)
> where the ROH would have gone.
>
> You only want an ROH if you have a lone oligosaccharide (or
> monosaccharide, etc.) that is not attached to a protein, etc.
> Otherwise, leap will get confused because there are too many atoms in
> the wrong places.
>
> The complaint about the HO1 indicates to me that leap doesn't know
> what to do with that atom (or, rather, the fact that it seems to be
> missing).
>
> If this doesn't help, and if you want to, send me your pdb and leap
> input files. If you want privacy, send them to me off-list. I'll see
> what I can do.
>
> :-) Lachele
>
>
> On 7/11/08, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
>>
>> 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
>> !
>> !ABORTING.
>>
>> -----------------------------------------------------------------------------------------------------------
>>
>> 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,
>> Waqas.
>>
>>
>> --- On Thu, 7/10/08, Lachele Foley (Lists) <lf.list_at_gmail.com> wrote:
>>
>> From: Lachele Foley (Lists) <lf.list_at_gmail.com>
>> Subject: Re: AMBER: [amber/glycam] dealing with fucose...
>> To: amber_at_scripps.edu
>> Date: Thursday, July 10, 2008, 10:24 AM
>>
>>
>> Waqas,
>>
>> 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 <nasirwaqas1983_at_yahoo.com> 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
>> 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
>> > -----------------------------------------------------------------------
>> > The AMBER Mail Reflector
>> > To post, send mail to amber_at_scripps.edu
>> > To
>> unsubscribe, send "unsubscribe amber" (in the *body* of the
>> email)
>> > to majordomo_at_scripps.edu
>> >
>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> 2-0263
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>>
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> 2-0263
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
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>
> 

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