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
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Received on Mon May 22 2023 - 07:51:50 PDT
