It seems that the optimization of the starting structure is not
converging. Perhaps it's best to first carry out a quick Molecular
Mechanics optimization of the initial structure. A nice program to do
this with a GUI is Avogadro, or you could use open-babel.
Are you happy to share the pdb file through here? That could speed up
the help we can give you,
Cheers,
Bruno
On 18/08/16 16:43, ATUL KUMAR wrote:
> here is some last lines of sqm.out file
>
>
>
> --------------------------------------------------------------------------------
> RESULTS
> --------------------------------------------------------------------------------
>
>
> QMMM: ERROR!
> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: E = -0.2388E+07 DeltaE = -0.1360E+04 DeltaP = 0.3567E+00
> QMMM: Smallest DeltaE = -0.5797E-01 DeltaP = 0.1462E+00 Step = 622
>
>
>
> *Atul Kuamr jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU,New Delhi
> India.
>
> On Fri, Aug 19, 2016 at 1:03 AM, Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
> wrote:
>
>> Your command seems OK.
>>
>> Check sqm.out, does it give a more informative message? Are you sure the
>> starting structure is OK?
>>
>> Hope this helps,
>>
>> Bruno
>>
>>
>> On 18/08/16 15:53, ATUL KUMAR wrote:
>>> Dear Urers,
>>> I am using antechamber for generating atomic charges and parameters for a
>>> ligand(Net charge is -4) molecules by the following command:
>>>
>>> antechamber -i Mol_red5.pdb -fi pdb -o Mol_red5.mol2 -fo mol2 -c bcc -s 2
>>> -nc -4
>>>
>>> after funning this i am getting following error message:
>>>
>>> Running: /home/atul_jaiswal/AMBER16/amber16/bin/bondtype -j full -i
>>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>>>
>>> Running: /home/atul_jaiswal/AMBER16/amber16/bin/atomtype -i
>>> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>>> Total number of electrons: 422; net charge: -4
>>>
>>> Running: /home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i sqm.in -o
>> sqm.out
>>> Error: cannot run "/home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i
>> sqm.in
>>> -o sqm.out" of bcc() in charge.c properly, exit
>>>
>>> Please help me out with this.
>>>
>>> *Atul Kuamr jaiswal*
>>> Research Scholar
>>> School of Computational and Integrative Sciences
>>> Centre for Computational Biology and Bioinformatics (CCBB)
>>> JNU,New Delhi
>>> India.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
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>>
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Received on Thu Aug 18 2016 - 13:00:04 PDT
