[AMBER] VMD not working after parmed

From: Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de>
Date: Mon, 30 Jan 2017 11:33:56 +0100

Hi all,

I am trying to modell a Peptide-Zinc system. As we do not know the
coordination of the Zn2+ ion I want to model it with the 12-6-4 Model.

I followed the tutorial and generated the C4 terms with parmed. I cannot
visualize the resulting parm7/crd files in VMD. Nor can I write the pdb
file with ambpdb.

In parmed I received the following warnings:

AmberWarning: Molecule atoms are not contiguous! I am attempting to
reorder the atoms to fix this.
AmberWarning: Residues cannot be part of 2 molecules! Molecule section
will not be correctly set. [Offending residue is 0: <Residue MOL[0]>]

M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059
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Received on Mon Jan 30 2017 - 03:00:03 PST
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