RE: AMBER: question about xwin load pdb file

From: Ross Walker <>
Date: Thu, 27 Jan 2005 21:38:30 -0800

Dear Xiaowen

> I installed AMBER8 on unix and installed X-win32 on windows
> computer. By using
> x-windows terminal,

I use this type of setup all the time so it shouldn't cause you and

>I follow everything from the tutorial 1
> to 3 to generate
> nuc.pdb, loadpdb and so on.
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> so far, everything is fine, same as the tutorial showed us.
> dna1=loadpdb "nuc.pdb"
> message as following:
> ============================================================
> dna1=loadpdb "nuc.pdb"
> (starting new molecule for chain T)
> --residue 536870912: duplicate [] atoms (total 438)

This is a very strange error. It suggests a corrupted pdb file. Can you post
me the nuc.pdb file that you are trying to load and I'll take a look. Also
download the pdb from the link on the tutorial page and compare it to the
one you made by following the steps in the tutorial. They should be
> edit dna1
> graphic window come out but did nothing. no graphy.
> Is the problem from my installation or from This X-windows,
> or others, like
> unix computer's memory (now it is 1 Gb)?

This is almost certainly a problem with the pdb file. Try running xleap as
stated in the tutorial and type edit LYS - it should come up showing you a
lysine residue.
> Then,
> I go to the $AMBERHOME/test/make test
> stop in
> cd qmmm/standard; ./Run.lysine
> =================================================
> exec():0509-036 cannot load program ../../../exe/sander.QMMM
> because of the
> following errors: 0509-026 system error: there is not enough
> memory available
> now.
> ./Run.lysine: Program error
> make: 1254-004 the error code from the last command is 1.

I take it all the tests before this passed. If they did then I wouldn't
worry about this test. You won't need sander.QMMM unless you want to run
QMMM calculations. You need to apply the bug fixes before you can use this.
You also need to increase the limits in your shell using the ulimit command.
For the moment I wouldn't worry about it.

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 - 05:53:00 PST
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