AMBER: format of .xyz files and pdb

From: Gobind Singh Bisht <>
Date: Thu, 1 Feb 2007 03:35:24 +0530

Dear friends,
                     my aim is to conduct a md using tinker binaries which i
built according to my needs. i have a pdb (which is basically a 3d array of
water molecules) which i wrote using a python code, after refering to pdb's
format. on trying to visualise it using VMD. However, i found that although
the basic array structure was correct, all the Oxygen atoms along columns
were bonded, etc. Also, i tried to load it on TINKER-FFE. This also failed.
On trying to convert the PDB into XYZ format using TINKER's binary, the
output was an empty file. Then i modified my program to output the XYZ file
directly. even then, neither VMD nor TINKER-FFE could load/display. I am
using amber99 parameters and tried different combinations of atom names like
"OH" (which is the one specified in the amber99 prm file in tinker suite)
and "O", etc. but to no avail. The xyz and pdb files are attached for
                      I understand that this is an AMBER group, but i would
request anyone who has played around with the file format, and visualization
of self-generated pdb's to please help me out.

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Received on Sun Feb 04 2007 - 06:07:19 PST
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