AMBER Archive (2005)

Subject: Re: AMBER: regarding ambpdb

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Thu Dec 01 2005 - 07:39:31 CST

thanks for your comments, i checked in VMD, it displays correctly, but i
don't know how to superimpose structures in VMD. pls help me in this regard

On 12/1/05, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
>
> 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,
> > CLRI
> > 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) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
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--
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830

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