[AMBER] GlcNAc-UDP problem with frcmod file

From: Sonia Romero <sromerte11.gmail.com>
Date: Fri, 25 Nov 2016 11:15:41 +0100

Good mornning everybody,

I'm working on a sugar residue GlcNAc covalently bonded to an UDP

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

the result is

Segmentation fault (core dumped)

I tried to do this from the mol2 file extracted from xleap after the

parmchk2 -i UGN_mod_leap.mol2 -f mol2 -o UGN_mod_leap.frcmod -p

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

Thank you in advance,


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Received on Fri Nov 25 2016 - 02:30:03 PST
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