Re: [AMBER] ligand molecule problem

From: Jason Swails <>
Date: Mon, 11 Mar 2013 09:18:14 -0400

On Sun, Mar 10, 2013 at 11:08 PM, tianchuan881 <>wrote:

> Dear amber,
> In my simulation process, the ligand molecule has broken into parts when I
> save new pdb files by the end of tleap. I re-checked my preparation process
> as follows. I hope you could help me solve this problem. The new pdb file
> and ligand files has been attached.

My guess is that the 'breaking into parts' is merely a visualization effect
and is not 'real'. If you are using VMD to visualize your PDB file (and
PDB files typically do not have CONECT records when written by tleap, if I
recall correctly), then VMD uses a simple distance-based criteria to
determine if atoms are bonded together or not. If your original PDB file
had CONECT records, then this would explain why the first structure had
bonds and the tleap PDB does 'not'.

The 'appropriate' test to see if bonds still exist is to load the topology
file and coordinate file directly into VMD (don't use the tleap-saved PDB
file). In this case, VMD will draw bonds according to those specified in
the topology file. So if the bond exists in the topology file, it will be
drawn there.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Mar 11 2013 - 06:30:04 PDT
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