Thanks for the reply!
I will be very thankful if you can send me detail of the prmtop file
formatting in order to do differential 1-4 scaling
Manoj
On Wed, Sep 8, 2010 at 5:14 PM, Lekpa Duukori <duukori.gmail.com> wrote:
> Hi,
>
> Amber 10 does differential scaling with PMEMD but you will need to
> edit the topology file by hand to make this work. In amber 11 it works
> automatically, you don't need a prmtop edit.
>
> I can forward you a workaround that I got from Ross.
>
> Lekpa
>
> On 9/8/10, manoj singh <mks.amber.gmail.com> wrote:
> > Thanks for the quick reply.
> >
> > The bugfix #26 for Amber10 says that PMEMD can do differential scaling.
> >
> > I will be very thankful for more information on this.
> >
> > Manoj
> >
> > On Wed, Sep 8, 2010 at 4:46 PM, Lachele Foley (Lists)
> > <lf.list.gmail.com>wrote:
> >
> >> Amber 10 (Ross - correct me if I'm wrong), does not read SCEE and SCNB
> >> parameters from the topology file. It is not possible to do mixed
> >> scaling of 1-4 parameters in Amber 10. For Amber 10, you still need
> >> to specify scee and scnb values in the mdin file.
> >>
> >> When you can not do mixed scaling, we recommend using the scaling
> >> appropriate to the protein (Amber, 10 or 11, scales for the protein by
> >> default). The 1-4 scaling mainly affects linkage torsions. In many
> >> bound-ligand situations, those torsions are fairly well constrained,
> >> so changes in populations is not of great concern. However, if the
> >> proper analysis of your situation requires detailed and accurate
> >> knowledge of those torsions, you would be better off using Amber 11.
> >> Note: if you switch to Amber 11, definitely delete the scee and scnb
> >> values from the input file.
> >>
> >> :-) L
> >>
> >> On Wed, Sep 8, 2010 at 4:30 PM, manoj singh <mks.amber.gmail.com>
> wrote:
> >> > 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
> >> >> >>
> >> >> > _______________________________________________
> >> >> > 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
> >>
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 08 2010 - 14:30:10 PDT
