Thank you very much for your response.
. I increased the cell dimension. This did not work.
I think the chamber tool is not generating the (.prmtop) properly.
Is there any other way to make the (.pdb) file compatible with AMBER (
means AMBER can recognize the residue)?
I tried with the antechamber too using gaff2, but it also failed to
generate the force field.
Any help would be appreciated.
Thank you!
Regards,
Pinky
On Mon, Feb 1, 2021 at 4:26 PM Pinky Mazumder <pmazumder67.gmail.com> wrote:
> Thank you very much. I increased the cell dimension. This does not work.
> I think the chamber tool is not generating the (.prmtop) properly.
>
> Is there any other way to make the (.pdb) file compatible with AMBER (
> means AMBER can recognize the residue)?
>
> I tried with the antechamber too using gaff2, but it also failed to
> generate the force field.
>
> Any help would be appreciated.
>
> Thank you!
>
> Regards,
> Pinky
>
>
> On Thu, Jan 28, 2021 at 3:00 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Thu, Jan 28, 2021, Pinky Mazumder wrote:
>> >> Common name cellulose
>> >> Formula C12 H14 O10
>> >> a 7.784 ± 0.008 Å
>> >> b 8.201 ± 0.008 Å
>> >> c 10.38 ± 0.01 Å
>> >> My unit cell dimension is a=7,78, b=8.2, c=10.38. alpha=beta=90 degree,
>> >> gamma=96.5degree.
>>
>> Look at the bottom of the inpcrd file, which shows the real unit cell
>> parameters:
>>
>> 17.1280000 36.8290000 43.5600000 90.0000000 90.0000000 90.0000000
>>
>> The "x" direction is only 17.1 Å, which is too small for Amber. If you
>> need
>> a periodic system, you need have more unit cellts in that direction.
>>
>> ....dac
>>
>>
>
> --
> Pinky Mazumder
> PhD Student
> University of Alabama
> USA
>
--
Pinky Mazumder
PhD Student
University of Alabama
USA
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Received on Mon Feb 01 2021 - 14:30:02 PST
