Thanks for the reply!
I do always check the structure, specially after doing minimization.
Manoj
On Wed, Sep 8, 2010 at 7:14 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> Unless you have a thiol linkage associated with your sugar, those are
> not relevant to you. But, thanks for pointing that out. They do
> represent some cleanup we need to do. I'll send the info to the
> relevant individual.
>
> If sleap didn't have all the information it needs, it would not have
> made top and crd files. So, it looks ok.
>
> That being said... do check the top & crd structures in VMD. Really.
> Do it. If you don't know how, this is a good time to learn.
>
>
>
> On Wed, Sep 8, 2010 at 6:31 PM, manoj singh <mks.amber.gmail.com> wrote:
> > Thanks for all the help!
> >
> > While generating the prmtop in sleap, I am getting following warnings,
> > otherwise things look good. Attached is the leap input and output.
> >
> > ------
> > Info: ignoring unknown atom type: NH
> > Info: while reading DIHE. Input: NH CG CG SM 1 0.45
> > 0.0 3. SCEE=1.0 SCNB=1.0
> > Thiol linkages
> > Info: ignoring unknown atom type: NP
> > Info: ignoring unknown atom type: NO
> > Info: ignoring unknown atom type: CX
> > -----
> >
> > Manoj
> >
> > On Wed, Sep 8, 2010 at 5:22 PM, Lekpa Duukori <duukori.gmail.com> wrote:
> >
> >> I will do that, but it seems the new version of AT maybe able to write
> >> this
> >> automatically if you use
> >>
> >> "set default write14scale on"
> >>
> >> PMEMD can then read the new SCEE/SCNB section in the prmtop.
> >>
> >> Lekpa
> >> On Wed, Sep 8, 2010 at 3:16 PM, manoj singh <mks.amber.gmail.com>
> wrote:
> >>
> >> > 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
> >> >
> >> _______________________________________________
> >> 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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Received on Wed Sep 08 2010 - 22:30:03 PDT
