AMBER Archive (2009)

Subject: [AMBER] Ligand covalent bonds appear to be broken

From: moitrayee_at_mbu.iisc.ernet.in
Date: Fri Oct 30 2009 - 01:32:39 CDT

Dear Amber Users,

I am facing a problem when visualizing my simulations with VMD. I am following
two methods:

1. I convert my crds to pdbs using ptraj. The script for it using the following
actions:

rms first out rms @CA
center @CA
image
strip :WAT

go

When I load this pdbs to VMD using animatepdbs.tcl script (available at VMD site
to load multiple pdbs), everything seems allright except my ligand, in which
some covalent bonds appear to be broken for the line or bond representation of
the ligand. However, using VDW sphere representation, I can see the whole ligand
intact.

2. I use another method for visualization. I directly load my trajectories to
VMD using the parameter files and crds. In this case, I find no such error.
Everything is perfectly fine in all representation types.

Is this some visualisation effect ? Please help me with your valuable
suggestions/comments.

Thanks a lot in advance.

Best Regards,
Moitrayee 

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