Many thanks for your kind suggestion.
Your guess is absolutely correct. I used "Amber coordiantes" as the file type for the inpcrd file to make the image using VMD. Now I will change it to "Amber7 restart". In my first/second mail I also mentioned that I have also created a pdb file using ambpdb and use that to load the coordinates. The corresponding structure is not showing such kind of unusual bonds.
Now another question, in case of visualization of the trajectory file (mdcrd file) which file type shall I choose "Amber7 restart" or "Amber coordiantes"?
If you dont mind I have another quarry why it is looking so when I use "Amber coordiantes" instead of "Amber7 restart" in VMD?
With my best regards
Sindrila
From: case <case.biomaps.rutgers.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Sent: Sunday, 29 May 2011 7:13 AM
Subject: Re: [AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS
On Sat, May 28, 2011, Sindrila Dutta banik wrote:
>
> I am hereby enclosing the modified pdb file (1ASZ_4.pdb) and the
> corresponding topology file (1ASZ_4.prmtop) as well as coordinate file
> (1ASZ_4.inpcrd) generated using the modified pdb file. I also attached a
> image of the corresponding part of protein which shows the long bonds
> between the chiral carbon atom and nitrogen atom of amino group of N
> terminal amino acid.Â
The problem must be with how you are using VMD to make the image, since the
input coordinates and prmtop file are fine. You should first load the prmtop
file (as an "Amber7 Parm") and then the inpcrd file (as an "Amber7 restart").
Or, create a pdb file using ambpdb, and use that to load the coordinates.
My guess(?) is that you were using "Amber coordiantes" as the file type for
the inpcrd file, which will not work.
...dac
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Received on Sat May 28 2011 - 22:30:02 PDT
