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
> >>> > >
> >>> > > _______________________________________________
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> >>> > > AMBER.ambermd.org
> >>> > > http://lists.ambermd.org/mailman/listinfo/amber
> >>> > >
> >>> > >
> >>> > _______________________________________________
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> >>> >
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> >>>
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> >>
> >
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Received on Thu Jun 04 2015 - 02:30:03 PDT
