Is the formatting not what sleap provides in the most recent AmberTools?
Check your topology file for entries "SCEE" and "SCNB". If they
aren't present, then you won't get mixed scaling. And see what Lepka
says...
On Wed, Sep 8, 2010 at 5:16 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
>>
> _______________________________________________
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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 - 14:30:14 PDT
