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
>
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- chemical/x-gamess-input attachment: leap.inp
- application/octet-stream attachment: leap.out
Received on Wed Sep 08 2010 - 16:00:03 PDT
