Dear Roopali,
I just wanted to warn you that you might have missed to include the Mg ions
in your initial protein complex. Mg2+ ions really matter when it comes to
ATP/ADP, which is your case. It could happen that you have simulated your
enzyme + ADP (without Mg ions) and ended up with the strange behavior that
you can not validate through available experimental data. To have a sense
of what I mean please read this year article in Nature structural &
molecular biology: The energy landscape of adenylate kinase during
catalysis doi:10.1038/nsmb.2941 and then following News & Views: An enzyme
cofactor with a split personality doi:10.1038/nsmb.2968. Authors have used
combination of NMR measurements during catalysis, pre-steady-state
kinetics, molecular dynamics simulations and x-ray crystallography to
describe adenylate kinase during catalysis. Also, you’ll find
results/behavior of the enzyme with and without Mg2+ ions present.
Thus, first thing to do is to prepare coordinates of complex. That means
that you have to figure out the optimal number of Mg2+ ions in the active
site and their positions (coordinates). I suppose that x-ray structure that
you took from the PBD database doesn’t contain Mg2+ ions, but that doesn’t
mean that Mg ions are not there in reality. It is unfortunately a common
problem because it is difficult to distinguish Mg2+ from structural water
by electron density alone, and therefore the position of the Mg2+ in the
presence of natural substrates is ambiguous and that is why x-ray protein
structures often miss coordinates for Mg ion(s).
So, I suggest you talk to your supervisor or to experimentalists and search
the literature or write to the authors of the paper you refer to in order
to find out optimal number of Mg ions. Check all the structures of your
enzyme or homologues of your enzyme deposited in PDB – maybe in one of them
you’ll find coordinates of Mg ion(s).
Finally, when you carefully prepare your initial complex.pdb, there are
more options for divalent metal ions like Mg. Search amber mailing list
archive
http://archive.ambermd.or to see what people ask and do when they
deal with Mg ions. Also as Marc already have pointed out you’ll find
parameters for ADP and ions here
http://www.pharmacy.manchester.ac.uk/bryce/amber/
Sandra
On Thu, Jun 4, 2015 at 11:20 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Dear Roopali,
>
> You need to make sure that the residue name and all atom names are exactly
> the same in your adp.lib or .prepc file.
> I would also strongly recommend using the specifically developed parameters
> for ADP (as I pointed out earlier) instead of ones generated by
> antechamber.
> The prepc & frcmod are free to download here:
> http://www.pharmacy.manchester.ac.uk/bryce/amber/
>
> Good luck,
> Marc
>
> On 4 June 2015 at 10:04, ROOPALI VERMA <roopaliverma7.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I have generated the ADP crd and top file from antechamber. But when I
> try
> > to generate the complex(with adp) crd and top file its shows error.
> > I used the following command:
> >
> >
> >
> > * /home/drpunit/amber12/bin/tleap -s -f
> > /home/drpunit/amber12/dat/leap/cmd/leaprc.ff99SB>source leaprc.gaff *
> >
> > >loadamberparams sustiva.frcmod
> >
> > >loadoff adp.lib
> >
> > >complex = loadpdb complex.pdb
> > >saveamberparm complex comp.prmtop comp.inpcrd
> >
> > it shows following error:
> >
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: -14.000000 is not zero.
> > FATAL: Atom .R<ADP 496>.A<PA 1> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<PB 2> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C5' 3> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O5' 4> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C4' 5> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O4' 6> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C3' 7> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O3' 8> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C2' 9> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O2' 10> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C1' 11> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<N1 12> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O1A 13> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O1B 14> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C2 15> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O2A 16> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O2B 17> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<N3 18> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O3A 19> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<O3B 20> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C4 21> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C5 22> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C6 23> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<N6 24> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<N7 25> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<C8 26> does not have a type.
> > FATAL: Atom .R<ADP 496>.A<N9 27> does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> > >
> >
> > when i have run the tutorial (
> > http://ambermd.org/tutorials/basic/tutorial4b/
> > ) it also shows the error.
> > If iam not wrong it doesn't take the parameters for the ligand.
> > Need Help
> >
> > Regards
> > Roopali
> >
> >
> >
> > On Thu, Jun 4, 2015 at 10:28 AM, ROOPALI VERMA <roopaliverma7.gmail.com>
> > wrote:
> >
> > > Dear Aleksandra,
> > >
> > > Thanks for ur reply.
> > >
> > > As u have said with adp/atp Mg ions should be added. if i add Mg ions,
> > > then how can i generate its crd and top files.
> > > Should i follow the antechamber protocol for mg ions as used for ADP.
> > > Please suggest.
> > >
> > > Regards
> > > Roopali
> > >
> > > On Thu, Jun 4, 2015 at 10:21 AM, ROOPALI VERMA <
> roopaliverma7.gmail.com>
> > > wrote:
> > >
> > >> Dear Marc,
> > >>
> > >> thanks for ur reply .
> > >> i have used -nc -3 and now it works.
> > >>
> > >> Regards
> > >> Roopali
> > >>
> > >> On Wed, Jun 3, 2015 at 3:06 PM, Aleksandra Skoric <
> > >> skoricaleksandra.gmail.com> wrote:
> > >>
> > >>> Dear Roopali,
> > >>>
> > >>> Also, be careful with the complex structure. You don't have Mg ions
> in
> > >>> your
> > >>> complex - ATP/ADP is always bound to an enzyme as a complex with Mg
> > >>> ion/s,
> > >>> so you have to include ion/s.
> > >>>
> > >>> P.S. for parametrization look at tutorial B4
> > >>> http://ambermd.org/tutorials/basic/tutorial4b/
> > >>>
> > >>>
> > >>> Sandra
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> On Wed, Jun 3, 2015 at 10:41 AM, Marc van der Kamp <
> > >>> marcvanderkamp.gmail.com
> > >>> > wrote:
> > >>>
> > >>> > Dear Roopali,
> > >>> >
> > >>> > The reason antechamber fails is quite clearly explained in the
> error
> > >>> > message:
> > >>> > "*Total number of electrons: 205; net charge: 0 *
> > >>> > INFO: Number of electrons is odd: 205
> > >>> > Please check the total charge (-nc flag) and spin
> multiplicity
> > >>> (-m
> > >>> > flag)"
> > >>> >
> > >>> > I haven't checked your pdb, but your diphosphate probably has a
> > formal
> > >>> > charge of -3 or so, so you should use antechamber with "-nc -3".
> > >>> >
> > >>> > More importantly, however, antechamber/GAFF is not really meant for
> > >>> > parameterising ADP. Luckily, others (Carlson et al., 2003) have
> > >>> developed
> > >>> > parameters that should (at the very least) be a good starting
> point.
> > >>> >
> > >>> > See here:
> > >>> > http://www.pharmacy.manchester.ac.uk/bryce/amber/
> > >>> >
> > >>> > You can donwload the prepc and frcmod files for ADP and ATP from
> > there.
> > >>> >
> > >>> > Good luck,
> > >>> > Marc
> > >>> >
> > >>> > On 3 June 2015 at 09:08, ROOPALI VERMA <roopaliverma7.gmail.com>
> > >>> wrote:
> > >>> >
> > >>> > > *Dear Amber Users, *
> > >>> > >
> > >>> > > *I want to simulate a protein structure docked with ADP and for
> ADP
> > >>> want
> > >>> > to
> > >>> > > generate its crd *
> > >>> > > *and top files. In order to do so I used ANTECHAMBER to generate
> > its
> > >>> > > mol2 **file
> > >>> > > calculate the charges and atom types. I used the following
> command.
> > >>> *
> > >>> > >
> > >>> > >
> > >>> > > *root.drpunit-Precision-WorkStation-T3500
> > >>> > > :/home/drpunit/Desktop/interdomain/dockadp#
> > >>> > > antechamber -i ADP.pdb -fi pdb -o adp.mol2 -fo mol2 -c bcc -s 2
> *
> > >>> > > *Running: /home/drpunit/amber12/bin/bondtype -j full -i
> > >>> > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC
> > >>> > > <http://ANTECHAMBER_BOND_TYPE.AC> -f ac *
> > >>> > >
> > >>> > > *Running: /home/drpunit/amber12/bin/atomtype -i
> ANTECHAMBER_AC.AC0
> > -o
> > >>> > > ANTECHAMBER_AC.AC <http://ANTECHAMBER_AC.AC> -p gaff *
> > >>> > >
> > >>> > > *Total number of electrons: 205; net charge: 0 *
> > >>> > > INFO: Number of electrons is odd: 205
> > >>> > > Please check the total charge (-nc flag) and spin
> > multiplicity
> > >>> (-m
> > >>> > > flag)
> > >>> > >
> > >>> > >
> > >>> > >
> > >>> > > *Running: /home/drpunit/amber12/bin/sqm -O -i sqm.in <
> > http://sqm.in>
> > >>> -o
> > >>> > > sqm.out *
> > >>> > > *Error: cannot run "/home/drpunit/amber12/bin/sqm -O -i sqm.in
> > >>> > > <http://sqm.in> -o sqm.out" of *
> > >>> > > *bcc() in charge.c, properly**, exit *
> > >>> > >
> > >>> > > Iam using Amber12 with Ambertools13.
> > >>> > > also attaching the pdb files of the ligand and the complex.
> > >>> > > what could be the possible reason.
> > >>> > >
> > >>> > > Please guide.
> > >>> > >
> > >>> > > Thanking in anticipation.
> > >>> > >
> > >>> > > Regards,
> > >>> > > Roopali
> > >>> > >
> > >>> > > _______________________________________________
> > >>> > > AMBER mailing list
> > >>> > > AMBER.ambermd.org
> > >>> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >>> > >
> > >>> > >
> > >>> > _______________________________________________
> > >>> > AMBER mailing list
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> > >>> > http://lists.ambermd.org/mailman/listinfo/amber
> > >>> >
> > >>> _______________________________________________
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> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > >
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Received on Thu Jun 04 2015 - 04:00:02 PDT
