I’ve attached the pdb and mol2 file I used as input to antechamber. I generated these files using xleap by modifying a cytosine nucleotide from OL15. The command I used for antechamber was:
antechamber -i zh.mol2 -fi mol2 -o zh-aa.mol2 -fo mol2 -c bcc -s 2 -at amber -rn ZZH
Thanks,
Reza
> On Sep 28, 2021, at 4:09 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Tue, Sep 28, 2021, Reza Esmaeeli wrote:
>>
>> I am trying to parametrize a nucleotide analog with a NO2 functional
>> group on the base. After running antechamber and getting the mol2 file, I
>> get the following error from parmchk2:
>>
>> Atom type of NO does not shown up in PARMCHK.DAT
>
> Can you say what command-line arguments you gave to antechamber and to
> parmchk2? Providing the input pdb file (or similar) that you gave to
> antechamber would also help.
>
> Atom types in capital letters (like NO) are supposed to be Amber atom types,
> but PARMCHK.DAT indeed knows nothing about NO. There are no NO2 functional
> groups in proteins or nucleic acids, so that is hardly suprising. But I don't
> know how you got a NO type assigned in the first place.
>
> If you came up with this "by hand", then you will need to prepare a frcmod
> file by hand as well. Use GAFF atom types (as a test) for your model. You
> will probably see atom type "no" (lower case) for your nitrogen. Copy
> parameters that involve it to the frcmod file, changing "no" to "NO" and
> adapting the atoms types of the atoms it is bonded to as needed.
>
> ...good luck...dac
>
>
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Received on Wed Sep 29 2021 - 10:30:02 PDT
