please send me PDB structure you actually give to antechamber
On Fri, Nov 25, 2011 at 6:33 PM, <fn1.rice.edu> wrote:
> 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/
>>>>
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>>>>
>>>>
>>>
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Dmitry Nilov
>> Faculty of Bioengineering and Bioinformatics,
>> Lomonosov Moscow State University
>> web: http://enzyme.fbb.msu.ru/
>>
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>> 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/
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Received on Fri Nov 25 2011 - 08:00:06 PST
