Hi Rodrigo,
In my case, the molecule looks like this,
CH3
|
-HC=N-CH=
+
Do you think Antechamber could not charge +1? What else could I do for
parameters of this ligand?
Thanks!
Fengyun
Quoting ros <rodrigogalindo.gmail.com>:
> Double check the number of protons (hydrogen atoms) on your molecule.
> Antechamber is detecting a combination of atoms that is not possible
> for the charge you want (1)
>
> Hope this helps.
>
> Rodrigo
>
> 2011/11/25, fn1.rice.edu <fn1.rice.edu>:
>> 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
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> --
> Enviado desde mi dispositivo móvil
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 25 2011 - 07:30:06 PST
