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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> > >
> > >
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Received on Wed Jun 03 2015 - 22:00:02 PDT
