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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Received on Fri Nov 25 2011 - 07:00:04 PST
