Good mornning everybody,
I'm working on a sugar residue GlcNAc covalently bonded to an UDP
nucleoside.
In order to obtain the parameters of this molecule, I performed a resp
calculation in gaussian09 for the charges of the whole ligand, then
generated a mol2 file,
opened it with xleap and manually changed the atom names and atom types to
that ones corresponding on the templates for 0VA of GLYCAM_06j-1.prep and
U3 of nucleic10.in .
Finally I save the prep file which is attached in this email.
when I check my ligand in xleap some parameters where missing, so I proceed
to use parmchk2 to generate the frcmod file.
I want to use the parameters from GLYCAM database.
$parmchk2 -i UGN_mod_attype_mod.prep -f prepi -o UGN_mod_leap.frcmod -p
$AMBERHOME/dat/leap/parm/GLYCAM_06j.dat
the result is
Segmentation fault (core dumped)
I tried to do this from the mol2 file extracted from xleap after the
modifications,
parmchk2 -i UGN_mod_leap.mol2 -f mol2 -o UGN_mod_leap.frcmod -p
$AMBERHOME/dat/leap/parm/GLYCAM_06j.dat
the result was
Atom type of Cg does not shown up in PARMCHK.DAT
for sure it is not taking the parameters from GLYCAM, Am I doing something
wrong?
Thank you in advance,
Sonia.
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Received on Fri Nov 25 2016 - 02:30:03 PST
