Priyasha,
I fear you provided too less information for sound support from the list.
You seem to parameterize a DNA-base derivative and to have used an atom
type that is already present in ff14SB, but with a different definition,
which might lead to complications.
Since parameter development is an advanced task in MD, solutions might
be depending on the respective system.
Maybe a critical review of your atom type assignment with potential
reassigning could be a first step towards useful parameters
(cf
http://archive.ambermd.org/202210/0026.html ),
but other list members might chime in here as well.
Good luck,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 28.08.2023 um 16:23 schrieb Priyasha Majee via AMBER:
>
>
> Dear All,
>
> I am working with DNA with some modifications. I need to find the
> missing parameters for the incorporated modification. For that I am
> using parmchk2 command but i am getting warning which goes like this.
>
> Warning: Atom type (CI) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> It is recommended to add the new atom type (CI) to PARMCHK.DAT.
>
> my input goes like this:
>
> parmchk2 -i CT-A_m1-c1_m2-c1.mol2 -f mol2 -o output.frcmod -p
> $AMBERHOME/dat/leap/parm/parm10.dat
>
> How can I resolve this?
>
> I checked the ff14SB library. it has CI sp3. but in my case it is CI
> sp2. Where am i going wrong?
>
> Thank you in advance for the guidance
>
> Priyasha Majee
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Received on Wed Aug 30 2023 - 01:30:03 PDT
