Thanks for the reply and guidance!
I have one last question about running simulation in PMEMD and 1-4 scaling.
I have used latest version of AmberTool-1.4 (which I have downloaded couple
of days ago) and applied latest patch to Amber10 and compiled PMEMD with
latest patch. Now, if I correctly understand, the parmtop file has the
differential 1-4 scaling information and if I run PMEMD without any explicit
information of SCNB and SCEE, it will do the differential 1-4 scaling for
protein and carbohydrate automatically.
I will be very thankful for the any response.
Manoj
On Wed, Sep 8, 2010 at 9:35 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> The procedure looks ok, but I definitely suggest inspecting the top
> and crd file directly using VMD. Most especially, be sure the bonds
> are all correctly placed. Doing this every time before you start a
> simulation can save you a world of headache. Since you call the
> glycan "ligand," I assume it is not covalently bound to the protein.
> If it should be bound, especially check that bond -- make sure there
> are no extra atoms (two oxygens in a row, 5 bonds to a carbon,
> etc...).
>
>
> On Tue, Sep 7, 2010 at 4:51 PM, manoj singh <mks.amber.gmail.com> wrote:
> > Thanks for your response!
> >
> > One more thing. Following is the command which I have used for creating
> the
> > protein-carbohydrate complex in amber. I will be very thankful if you can
> > look over it.
> >
> > ---
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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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 Wed Sep 08 2010 - 14:00:03 PDT
