Re: [AMBER] GLYCAM residue naming

From: manoj singh <mks.amber.gmail.com> Date: Tue, 7 Sep 2010 16:51:39 -0400

---
tleap -s -f leaprc.ff99SB
source leaprc.GLYCAM_06
com = loadpdb PRA_crd1.pdb
bond com.111.O1 com.112.C1
bond com.112.O3 com.113.C1
bond com.112.O6 com.114.C1
check com
solvateOct com TIP3PBOX 12.0
charge com
addions com K+ 0
addions com Cl- 0
saveamberparm com pra_crd1_solvated.prmtop pra_crd1_solvated.inpcrd
---
Manoj
On Tue, Sep 7, 2010 at 10:05 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
> >>
> >
> > _______________________________________________
> > 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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>
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