Dear Amber users
I'm trying to figure out if and what parameters might be missing from my
prep-file for modified nucleic acids, but parmchk2 (and parmchk) are giving
me the same error message: 'Invalid atom name (C3') in the LOOP section.'
This is for the first defined residue, namely an adenosine nucleotide which
has three explicating loop closings defined as the following:
.
LOOP CLOSING EXPLICIT
C3' C4'
C4 C5
C4 N9
DONE
This is how I call parmchk2:
parmchk2 -i *.prep -o frcmod -f prepi -p PYRed.frcmod
which errors in:
Invalid atom name (C3') in the LOOP section
The thing is: I wanted to change an atom type from a sugar-phosphate
backbone carbon atom (somewhat like the DNA.OL15-modification) in order to
more accurately parametrize backbone dihedrals (using QM) for these modified
nucleic acids and wanted parmchk to list the missing parameters after
changing the atom type. The initial frcmod was obtained using the
PYRed-server which also did the RESP charge fitting.
If I change the atom names, the problem persists and if I remove the " C3'
C4' " line entirely it just continues the error with the next loop closing
defined. Normally the prep-file shouldn't contain any error (leap generates
prmtop- and inpcrd-files just fine). So I was wondering if parmchk has a
problem reading loop closings? I couldn't find anything with regards to my
question on the web, so hopefully someone might point me in the right
direction.
Kind regards and thanks in advance
Charles-Alexandre Mattelaer
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Received on Fri Jul 14 2017 - 02:30:03 PDT
