Hi Dr. Case,
I was wondering if you had a chance to look at my mol2 and my prepc files?
I am still not sure if I am doing something wrong when generating those
prepc files.
Thanks,
Yuliana
On Sun, Jul 29, 2018 at 10:23 AM, Yuliana Bosken <ydavi002.ucr.edu> wrote:
> Hi,
> Thank you for your reply. Attached are the mol2 file and the two versions
> of prepc file that I get. We use Amber16 and AmberTools16, I may have
> upgraded to AmberTools 17 on one of the computers I am using but I am not
> quite sure and I don't know how to check the version.
> Thank you,
> Yuliana
>
> On Sun, Jul 29, 2018 at 5:13 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Sat, Jul 28, 2018, Yuliana Bosken wrote:
>>
>> > I used antechamber to generate charges for my ligand. However, for some
>> > reason when I select gaff for atom type I get different charges than
>> gaff2.
>> > Is that normal or I am doing something wrong?
>>
>> Thanks for the report.
>>
>> Can you post the igp.mol2 file you are using as input, so we can explore
>> this behavior? (I could convert prepc files, but you only gave a part
>> of the prepc file, so it would be best to make sure I'm using the same
>> inputs that you are.)
>>
>> Also, please let us know which version of AmberTools you are using.
>>
>> ...regards...dac
>>
>>
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>
>
>
> --
> Yuliana Bosken
>
--
Yuliana Bosken
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Received on Mon Jul 30 2018 - 11:30:02 PDT
