Re: [AMBER] problem in running sander

From: David A. Case <>
Date: Thu, 19 Mar 2009 12:13:11 +0000

On Thu, Mar 19, 2009, Kshatresh Dutta Dubey wrote:
> Here i am attaching the test results , there are some errors in
> mdout.tip5P, gcg.dip.o, nc_headers, first.pdb or run ambpdb. These test
> results are attached in the above file. How can i remove these errors???

You need to look at the individual files. I'm strongly guessing that
these are innocuous differences between platforms.

cd jar && ./Run.jar
java -jar ./Run.jar

Invalid or corrupt jarfile ./Run.jar
The execution of ./Run.jar failed. The reason is probably that ./Run.jar doesn't contain the MainClass in MANIFEST.MF.
If you want to unpack ./Run.jar, call:
 jar -xf ./Run.jar
cd plane_plane_restraint && ./Run.dinuc_plpt

[Hey, Adrian: have you folks seen this before? Looks like some platforms
stongly think that "jar" files imply java. ([On Ubunutu, if I try to "vi
Run.jar" the editor complains that this is not a zipfile!) We should
probably rename these files just to avoid problems like this one....]


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Received on Fri Mar 20 2009 - 01:15:04 PDT
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