Hi Dear all
I am trying to obtain topology and coordinates files for a simulation.
The molecule is p-nitrophenyl-B-D-glucopyraanose. I got SDF file from
pubchem, obtained pdb format with avogadro, and for frcmod I used
antechamber/ parmck2. Until this step everything is Ok.
So I docked the p-nitrophenyl-B-D-glucopyranose to a molecule and save
coordinates, however, when I tried to obtain topology and coordinates files
for the complex, there is an advice and tleap can´t build them.
The advice is the next:
Error: Atom .R<UNL 1>.A<C9 19> has force field coordination 4
but only 3 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon (if running interactively).
Error: Atom .R<UNL 1>.A<C11 21> has force field coordination 4
but only 3 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon (if running interactively).
Segmentation fault (core dumped)
The p-nitrophenyl group has an aromatic ring, so I think there should be C'
carbons, but I don´t know why antechamber assign C9, C10,C11, C12 atom
names.
Can somebody help me?
I appreciate it. Thanks on advance
Regards
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Received on Thu Mar 06 2025 - 12:30:02 PST
