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