Re: AMBER: problem related to visualizing of structure

From: Vlad Cojocaru <>
Date: Tue, 10 Apr 2007 10:25:06 +0200

Hi Deepti,

which version of VMD are you using?? Did you try to load the .top and
.crd files or only the .pdb file ?

Old versions of VMD would add bonds based on a trivial distance
criteria, so if you load a pdb file into an old VMD version, you will
get some "strange" bonds , especially since the structure created with
Leap is not a minimized structure ...

My advice is to try to load into VMD the initial topology and coordinate
files created by Leap instead of the pdb file. If the visualization will
show you again strange bonds, then it is likely that something is wrong
with your structure ....

If I were you, I would also use VMD 1.8.6 - the latest VMD version ...

Good luck

deepti nayar wrote:

> hi
> I have made a dipeptide using xleap. my peptide is a non-standard
> residue and so i saved the library first and then made the structure.i
> have added suitable bonds and atoms as per my requirement. but when i
> visualize it using vmd, i could see some unnecessary bondings there. i
> was wondering if there is some mistake in the structure that i built
> using xleap. its a phenylalanine-dehydrophenylalanine dipeptide.(i
> have added the double bond between alpha carbon and beta carbon in
> dehydrophenylalanine)
> i would be obliged if somebody tells me where is the problem
> thanks
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Apr 11 2007 - 06:07:35 PDT
Custom Search