Re: AMBER: format of .xyz files and pdb

From: Steven Winfield <>
Date: Wed, 31 Jan 2007 22:20:43 +0000


Atomeye ( or for version 3) opens
and displays the pdb fine.


Gobind Singh Bisht wrote:
> 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 review.
> 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.
> --
> gobind
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Received on Sun Feb 04 2007 - 06:07:19 PST
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