In the chemical structure, I think each phosphate should carry a
negative charge. Antechamber does not give it net charge, either. I
don't have experience in parameterization of ligand like this, so I
don't know whether the way Antechamber does is feasible. Do you think
it's all right to keep the net charge zero on the methylated nitrogen
atom?
Thank you!
Fengyun
Quoting Dmitry Nilov <nilovdm.gmail.com>:
> Do you consider negative charge on phosphates?
>
> On Fri, Nov 25, 2011 at 5:53 PM, <fn1.rice.edu> wrote:
>> Hi,
>>
>> Thanks for reply!
>>
>> When I did not use the -nc option as follows,
>> antechamber -i GTG-align_h.pdb -fi pdb -o gtg.mol2 -fo mol2 -c bcc -nc -s -2
>>
>> Info: Bond types are assigned for valence state 5 with penalty of 1
>>
>> Total number of electrons: 412; net charge: 0
>>
>> Everything goes fine.
>>
>> But when I included a -nc option as follows,
>> antechamber -i GTG-align_h.pdb -fi pdb -o gtg.mol2 -fo mol2 -c bcc
>> -nc 1 -s -2
>>
>> Info: Bond types are assigned for valence state 5 with penalty of 1
>>
>> Total number of electrons: 411; net charge: 1
>> INFO: Number of electrons is odd: 411
>> Please check the total charge (-nc flag) and spin
>> multiplicity (-m flag)
>> Error: cannot run "/opt/apps/amber/11/bin/sqm -O -i sqm.in -o sqm.out"
>> of bcc() in charge.c properly, exit
>>
>>
>> Since the charge is on the nitrogen atom, do i need to add some
>> special options?
>>
>> Thanks!
>> Fengyun
>>
>>
>>
>>
>> Quoting Dmitry Nilov <nilovdm.gmail.com>:
>>
>>> I suppose you should use -nc option (net charge) of antechamber if
>>> parametrized molecule has non-zero charge.
>>>
>>> On Fri, Nov 25, 2011 at 5:17 PM, <fn1.rice.edu> wrote:
>>>> Hi,
>>>>
>>>> I want to generate the parameter with Antechamber for
>>>> 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE, where the pdb 1st0
>>>> contains this ligand. The question
>>>> is that this ligand has 7-methyl group on its nitrogen, which makes it
>>>> have a one
>>>> positive formal charge. However, Antechamber could not detect the
>>>> charge here and
>>>> regard the whole ligand as a neutral one.
>>>>
>>>> Could anyone please give some suggestions on this?
>>>>
>>>> Thank you very much!
>>>> Regards,
>>>> Fengyun
>>>>
>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>> Dmitry Nilov
>>> Faculty of Bioengineering and Bioinformatics,
>>> Lomonosov Moscow State University
>>> web: http://enzyme.fbb.msu.ru/
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>>
>>
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>>
>
>
>
> --
> Dmitry Nilov
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
> web: http://enzyme.fbb.msu.ru/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Nov 25 2011 - 08:00:04 PST
