AMBER Archive (2005)

Subject: AMBER: question about tleap load pdb file

From: xiaowen (xwfang_at_iastate.edu)
Date: Wed Feb 02 2005 - 21:19:19 CST

Dear Ross,

Since I cannot locally run Xwin, I try to use tleap.
Could you please see the attachments about the whole process?

Thanks and best regards!
xiaowen

> 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
> $AMBERHOME/dat/leap/cmd/leaprc.ff99
>
> 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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
>
>
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xiaowen

Chemistry Department
Iowa State University
Office phone number: 515-294-4285



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