Re: [AMBER] Problem in charge generation through antechamber

From: Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
Date: Fri, 19 Aug 2016 11:47:05 -0300

Hi. I attach the mol2 files with bcc charges and gaff atom types that I
obtained.

As you found out, the sqm optimization didn't converge since you have a
really large molecule. I used mopac instead for the AM1 optimization. I
attach the .mop input file.

Then I extracted the Mulliken charges obtained with mopac and generated
a new .mol2 file to feed into am1bcc to obtain the bcc charges by
following these commands:

antechamber -i aco1_opt-am1_mulliken.mol2 -fi mol2 -o
aco1_opt-am1_mulliken.ac -fo ac

am1bcc -i aco1_opt-am1_mulliken.ac -o aco1_opt-am1_bcc.ac -f ac -j 5

antechamber -i aco1_opt-am1_bcc.ac -fi ac -o aco1_opt-am1_bcc.mol2 -fo
mol2 -j 5


Hope this helps!

Bruno


On 19/08/16 03:11, ATUL KUMAR wrote:
> Thank you for reply. please find attached pdb file
>
> *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 1:28 AM, Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
> wrote:
>
>> 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
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Received on Fri Aug 19 2016 - 08:00:02 PDT
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