RE: AMBER: question about xwin load pdb file

From: Ross Walker <>
Date: Fri, 28 Jan 2005 10:20:18 -0800

Dear Xiaowen

I have verified that there is nothing wrong with your pdb file by following
the steps:

1)Copy your nuc.pdb file from the email to my desktop in windows.
2)FTP the file to my home directory on a linux machine.
3) Start up xwin32 v5.1 on my windows machine - configured in Multiple
window mode, tray icon selected in "multiple settings". It is configured as
display 0 on the ip address of my network card.
4) Ssh login to my linux machine using secure CRT - ensuring that "forward
X11 packets is turned on"
5) Run xleap - $AMBERHOME/exe/xleap -s -f

Up pops an xleap window on my windows machine.

6)Load the PDB file: test=loadpdb nuc.pdb
7) The pdb file loads with errors matching those in the tutorial (due to no
ter cards).
8) edit test

Up pops a window showing the DNA.

> x-win32 also do nothing on the screen. Edit LYS gives me same

When you say nothing here, what exactly do you mean? Does the initial xleap
window come up when you run it? Can you get other windows, e.g. xterm to
come up properly?
When you edit LYS do you get the unit viewer window but with no unit showing
or does the window not come up at all?

A couple of things to try:

1) Can you log in locally to the machine and get it to work? This will
isolate whether it is a problem with the xwin32 setup or with the
installation of xleap itself.

2) Can you try tleap. You won't be able to do any of the graphical
manipulation but you should be able to follow through the tutorial and get a
prmtop file out the other end. This will verify that the "back end" part of
xleap is working on your system.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Fri Jan 28 2005 - 18:53:00 PST
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