AMBER: regarding ambpdb

From: S.Sundar Raman <>
Date: Thu, 1 Dec 2005 16:10:58 +0530

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,
ph: 044-24411830
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Received on Thu Dec 01 2005 - 10:53:01 PST
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