You won't be able to build this with our builder, not even the new one
(the new one can add an acetyl group, but not yet yours).
First, a question (rhetorical): are you sure of the structure you
sent? You say there is a lactic acid attached, but the derivative
appears to be missing a hydroxyl group (if it is, indeed, lactic
acid). You don't really have to answer. It doesn't matter to this
situation. I just want to make sure you know what you're building.
Second: I believe you have slightly misunderstood our naming
convention. You should use 0YB rather than 1YB. The special residue
1YB is intended for anomeric-anomeric linkages, e.g., {0YB 1YB}.
For the bonding, you will have to be very specific with leap.
Something like the following should work if building up from residues:
m = sequence { ROH WYB }
set m tail m.2.O3
m = sequence { m LAC }
set m tail m.2.O4
m = sequence { m 0YB }
If you have coordinates in a PDB file, similar to what you sent me,
place a TER card after WYB and 0YB. That is, put a TER card after
each branch point and after each branch end. Then, issue explicit
bond commands in leap to reconnect them:
m = loadpdb structure.pdb
bond m.3.C1 m.2.O4
bond m.4.CA M.2.O3
Definitely do this:
charge m
...to see if your charges add to zero. If not, then you will need to
adjust them. In any case, validate your structure and charges against
whatever experimental values you can find.
On Mon, Dec 17, 2012 at 6:27 AM, Krisztina Feher
<feher_krisztina.yahoo.com> wrote:
> Hi Lachele,
>
> Thanks for the reply! As Francois suggested, charges I should be able to get from the RED server. For using the GLYCAM parameters I need to use the GLYCAM residues and atom types. For the first bGlcpNAc I used 1YB-1, then I made muramic acid as GlcpNAc with 3 connections: on position 4 the first NAG is connected, position 1 terminated with an OH and on position 3 lactic acid is attached. So I used WYB-2, ROH-3 and a LAC-4, but the bonds are not generated correctly between them in leap after loading the pdb file. I am just only learning how leap works and here I need a branch and I do not know how to make it. Do I have to manually edit the bonds in leap? Are the residue types I used correct?
>
> I tried the GLYCAM oligosaccharide builder, understandably there was no lactic acid, but also I did not find a way to make a branch on position 3 as there were only linkages from position 1 or 2.
>
> Thanks a lot in advance!
> Krisztina
>
>
>
> --- On Sun, 12/16/12, Lachele Foley (Lists) <lf.list.gmail.com> wrote:
>
> From: Lachele Foley (Lists) <lf.list.gmail.com>
> Subject: Re: [AMBER] branched disaccharide in leap
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, December 16, 2012, 4:01 AM
>
> We don't have structural and charge information for muramic acid. I'm
> not aware that anyone in the group is working on it either. Our
> parameters should work, but you would need to develop charges.
>
>
> On Sat, Dec 15, 2012 at 5:16 PM, Aron Broom <broomsday.gmail.com> wrote:
>> Have you considered using the Glycan builder by the group that makes the
>> AMBER Glycam forcefield (Woods group)?
>>
>> You can find their main website here http://glycam.ccrc.uga.edu/ccrc/
>>
>> Follow the amber utilities or somesuch and then carbohydrate builder or
>> something. This will allow you to not only generate a PDB easily, but all
>> the residues will have the appropriate names.
>>
>> ~Aron
>>
>> On Sat, Dec 15, 2012 at 3:25 PM, Krisztina Feher
>> <feher_krisztina.yahoo.com>wrote:
>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Dear All,
>>>
>>>
>>>
>>>
>>>
>>> I am trying to generate a disaccharide consisting
>>> bGlcpNAc[1,4]aGlcpNAc[3-]-lactic acid in leap, see in the attched pdb file.
>>> Could someone suggest me the monosaccharide units I should use for
>>> this molecule? My own attempt from 4 residues ROH 1, WYB 2, 1YB 3 and
>>> a self-constructed LAC 4 residue has incorrect connections, please, see
>>> the screenshot of molecule in the editor.
>>>
>>> GlcpNAc[3-]-lactic acid is in fact muramic
>>> acid, but I did not see separate PDB code for in the GLYCMA06.prep
>>> file, so I made it from GlcpNAc and a lib file for lactic acid in
>>> antechamber with gaff atomtypes. Is there a better way for muramic acid?
>>>
>>>
>>>
>>>
>>>
>>>
>>> Thanks in advance,
>>>
>>> Krisztina
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Dec 17 2012 - 12:30:02 PST
