Re: AMBER: regarding ambpdb

From: Ilyas Yildirim <>
Date: Thu, 1 Dec 2005 05:54:03 -0500 (EST)

Dear Raman,

Do u use the trajectory file (.mdcrd) or the restart file (.rst) to create
the .pdb files? For the second case, using ambpdb will create the correct
..pdb file. Do u use the following command to create it?

ambdpdb -p molecule.prmtop <molecule_min.crd> molecule_min.pdb

where molecule.prmtop is the topology file, molecule_min.crd is the
minimized restart file and molecule_min.pdb is the .pdb file of the
minimized structure.

Did u try to check these structures in VMD? In InsightII, it is normal if
it will show u a different structure, as it uses its library to define the
residues. Check out molecule_min.pdb. The atom names, the residue names
might look different than the residue library of InsightII. But I never
had any trouble in VMD. Try to check those minimized structures in VMD.

Good luck,

On Thu, 1 Dec 2005, S.Sundar Raman wrote:

> dear amber friends,
> i like to get structures from MD file at several snapshots, i used ptraj
> command to get that and then i used sander to remove the kinetic energy by
> minimize those structures. in order to align these structures i need the
> minimized coordinates in pdb format. hence i used ambpdb command to convert
> crd files which was minimized, to pdb file.( i used the topology file!).
> when i viewed the generated pdb file in pymol, insightII, and moil-view it
> showed the atoms connected very wrongly. but when i use ptraj to generate
> pdb file form the same topology and crd file, it produces correctly
> connected pdb file. why this kind of problem appears? pls help me in this
> regard. thank you
> --
> S.Sundar Raman
> Chemical Lab,
> Chennai-20
> ph: 044-24411830

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
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Received on Thu Dec 01 2005 - 11:53:01 PST
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