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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Dmitry Nilov
>> Faculty of Bioengineering and Bioinformatics,
>> Lomonosov Moscow State University
>> web: http://enzyme.fbb.msu.ru/
>>
>> _______________________________________________
>> AMBER mailing list
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>> 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 - 07:30:05 PST
