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