Dear David,
Thanks for your reply! I started my parameterization from the 1W5.cif file from PDB. I used the following commands:
1. antechamber -fi ccif -i 1W5.cif -bk 1W5 -fo ac -o 1w5.ac -c bcc -at amber
2. prepgen -i 1w5.ac -o 1w5.prepin -m 1w5.mc -rn 1W5
3. parmchk2 -i 1w5.prepin -f prepi -o frcmod.1w5 -a Y -p dat/leap/parm/parm10.dat
The ’NO’ atom type is generated in the output 1w5.prepin file from step 2. Also there are two atoms (‘ON1’ and ‘ON2’) with atom type ‘DU’. The corresponding files are attached.
Best regards,
Jiaan
> On Oct 9, 2022, at 12:34 AM, David A Case via AMBER <amber.ambermd.org> wrote:
>
> On Thu, Oct 06, 2022, Jiaan Zhu via AMBER wrote:
>>
>> I’m trying to parametrize a nucleotide analog(named 1W5 in PDB), and when
>> I run the following parmchk2 command ' parmchk -i 1w5.prepin -f prepi -o
>> frcmod.1w5 -a Y -p dat/leap/parm/parm10.dat', it raised an error 'Atom type
>> of NO does not shown up in PARMCHK.DAT’.
>
> You don't say what you started from to make the parameterization.
> Presumably(?) the "NO" atom type came from that choice. In older Amber
> force fields, atom type NO was equivalenced to N* and NC and NP. etc. So
> you can probably change your NO atom type to one of those. This is a bit of
> a guess in the absence of more information.
>
> ....dac
>
>
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- application/octet-stream attachment: 1W5.cif
- application/octet-stream attachment: 1w5.mc
- application/octet-stream attachment: 1w5.ac
Received on Sun Oct 09 2022 - 01:30:03 PDT
