Ross adds the following (separate email):
===================================
Hi Manoj,
If you applied bugfix.26 then PMEMD (and only PMEMD) should read the
variable 1-4 scaling info from the prmtop file. Specifically look for the
following in the output file:
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
If you do NOT see this printed in the output file then you will NOT be
running with the correct 1-4 scaling.
All the best
Ross
==================================
On Wed, Sep 8, 2010 at 4:51 PM, 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
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 08 2010 - 14:30:08 PDT
