Hello!
As far as I can see, you do not need an frcmod file, I ran your
molecule through tleap and it generated the topology and coordinates
just fine.
Rodrigo
On Mon, May 22, 2023 at 7:40 AM Robert Heße via AMBER <amber.ambermd.org> wrote:
>
> Hello,
>
> i want to parametrized modified guanine derivatives to be inserted into
> larger DNA strains. For an accurate description of these i wanted to use
> OL15 as much as possible and decided to see if any parameters are
> missing. As such i decided to generate myself a mol2 with charges via
> leap:
> "source leaprc.DNA.OL15
> savemol3 DG DG_ol15.mol2 1
> quit"
> This worked without an error and the mol2 looked fine as well even
> though just in case i attached it.
> When i tried to use parmck2 to generate myself a frcmod file, i got the
> following error:
> "parmchk2 -f mol2 -i DG_ol15.mol2 -o DG_ol15.frcmod -frc ol15"
> "Warning: Ignoring Mol2 record type (@<TRIPOS>HEADTAIL).
> Warning: Ignoring Mol2 record type (@<TRIPOS>RESIDUECONNECT).
> Atom type of CJ does not exist in PARMCHK.DAT"
> As far as i can see, all atom types of OL15 are missing in the
> PARMCK.DAT file. How do i best proceed? I was thinking of defining both
> the C7 and CJ atom type in a copy of PARMCHK.DAT but im unsure how i
> could define both. Or perhaps i could check which standard Amber and
> gaff2 atom types are most fitting for the missing atom types?
>
> With best Regards,
> Robert Hesse_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon May 22 2023 - 09:30:02 PDT
