Sahar,
the error you obtained indicates a deeper problem with your system:
The atom type assignment is probably not correct.
When you look into the pqr and prep file you attached you see that a
carbon and two hydrogen atoms have the DU (=dummy) atom type, which is
obviously not ok. Thus, you don't want to add the DU atom type to any
DAT file, but correct the atom types.
Although I can only guess how you created the prep file, I strongly
recommend to always have a look at automatically assigned atom types; in
the case of doubt, you could have a look into the original literature
for the exact atom type definition, but also the AMBER parameter files
contain a short definition of the atom types (thanks for the
documentation to the developers!). Be aware that the choice of the atom
type essentially directs all the other automatic parameter assignments
for bonds, angles, torsions and is key in ligand parameterization.
The DU atoms in your system are C26, HC26, H261. I tried to visualize
your system, and found that carbon C26 seems to have five valencies, two
of which are HC26 and H261. Thus, maybe your ligand structure needs a
closer look first.
Good luck!
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 10/27/2021 01:38 AM, Rohanizeidanlou, Sahar wrote:
> Hi Amber Community,
>
> I am running parmchk2 on a ligand structure after generating the .prep file using ANTECHAMBER and getting the below error:
>
>
> $AMBERHOME/bin/parmchk2 -i lig.prep -f prepi -o lig.frcmod
>
> Atom type of DU does not shown up in PARMCHK.DAT
>
> I know that the DU atom type does not exist in the PARMCHK.DAT file. Can anyone guide me how can I add this atom type in the DAT file?
>
> I have attached the ligand structure and prep file for your reference.
>
> Thanks for your support in advance.
>
> Best regards,
> Sahar Cain
>
>
>
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Received on Wed Oct 27 2021 - 01:00:02 PDT
