Your procedure looks fine, as does the mol2 file.
You can also check the top and crd files directly in VMD. First load
the top as "Amber parm6". Then, into the same molecule, load the crd
file as "Amber restart".
On Mon, Sep 6, 2010 at 9:56 PM, manoj singh <mks.amber.gmail.com> wrote:
> Thanks for your reply!
>
> So here is what I did.
>
> First, I formatted the lig.pdb into its current form (attached).
>
> Then I used following commands
>
> ----
>
> tleap -s -f leaprc.GLYCAM_06
>
> com = loadpdb lig.pdb
>
> bond com.1.O1 com.2.C1
> bond com.2.O3 com.3.C1
> bond com.2.O6 com.4.C1
>
> saveamberparm com lig_tmp.top lig_tmp.crd
> savepdb com lig_tmp.pdb
>
> ----
>
> I then used top2mol2 command to create lig_tmp.mol2 file from top and crd
> files.
>
> The structure I am getting looks good, however, I yet to run the MD.
>
> I will be very thankful if you can cross-check this procedure.
>
> Manoj
>
> On Mon, Sep 6, 2010 at 12:24 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> The structure in the pdb file you attached is:
>>
>> a-D-Manp-(1-3)-[a-D-Manp-(1-6)]-a-D-Manp-(1-)-OH
>>
>> In other words, a single alpha D mannopyranose has two others attached
>> at its 3 and 6 positions. If that is what you want, and I think
>> perhaps it is, then the structure is correct.
>>
>> To read the pdb into leap, you will need to place TER cards (in the
>> pdb file) between each of your residues then manually link them back
>> together in the proper order using the bond command within leap. When
>> a residue (your first one, VMA), is attached to more than one other
>> residue, leap is not always able to identify the attachment points for
>> subsequent residues. Inspection using VMD tells me that residue 2 is
>> attached at the three position and residue 3, at 6. You should also
>> terminate at the end of each chain (e.g., the 0MA), because if not,
>> you are essentially telling leap to bond that residue to the next one,
>> which is not what you want. Leap will happily do whatever you tell it
>> to do without regard to chemical sense (this is a good thing, but one
>> must respect it).
>>
>> There are further instructions for building a glycoprotein in the
>> AmberTools manual. The online glycoprotein builder should be
>> functional again in a day or two.
>>
>> :-) Lachele
>>
>>
>> On Mon, Sep 6, 2010 at 12:05 PM, manoj singh <mks.amber.gmail.com> wrote:
>> > Hi,
>> >
>> > I want to simulate a protein-carbohydrate system using ff99SB and GLYCAM
>> in
>> > Amber10. I am little confused over various issues with GLYCAM. First is
>> the
>> > residue nomenclature.
>> > I want to simulate {alphaMAN-1-->6-alphaMAN-3-->1-alphaMAN}. The
>> structure
>> > of the ligand is attached with the mail. Attached is the PDB file with
>> > residue name, which I think is consistent with the GLYCAM. I will be
>> very
>> > thankful if someone can verify this.
>> >
>> > Manoj
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
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>
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Sep 07 2010 - 07:30:06 PDT
