creating a solvent box

From: Bimo Ario Tejo <>
Date: Tue 06 Aug 2002 19:23:13 +0200

Dear Amber users,

I have problem when creating a CCl4 solvent box. I have equilibrated the solvent and got file. I converted it into ccl4box.pdb file using ambpdb (with new2oldparams). Up to this stage I have no problem

Then I loaded the .pdb file into xleap with its frcmod.ccl4 and ccl4.prep file. When I check the geometry, everything is OK, so I save it as ccl4box.lib and quit.

But then, when I loaded this ccl4box.lib into xleap again and check its geometry, xleap said there's no parameters for my solvent box. What's wrong? I have checked its geometry before save it as .lib file, but why when I loaded again into xleap seems all the parameters gone? Or I did a wrong protocol?

Any help is greatly appreciated.


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From 6 Aug 2002 17:29:48 -0000
Message-id: <>
Date: 6 Aug 2002 17:29:48 -0000
From: Jim <>
To: AMBER list <>
Subject: Re: "number of processors must be a power of two"
In-Reply-to: <&quot;number of processors must be a power of two&quot;>
Yes, that helped. Thank you. Looks like I might try something besides 
MPICH. Performance is definately suffering with that compile option. 
Thanks again.
> On Tue, Aug 06, 2002, Jim wrote:
> > 
> > number of processors must be a power of 2, and no greater than 128:
> This is a message generated by sander; with the (default) BTREE 
option in
> version 7, the number of processors indeed must be a power of 2.  It 
> nothing to do with your MPI implementation.
> You can remove this restriction by adding "-DnoBTREE" to your 
> variable (in the MACHINE file) and re-compiling.  This change might 
> even cost much in performance if your MPI has a good implementation 
of global
> gather/scatters (MPICH does not have very efficient implementations 
> ..hope this helps...dac
> -- 
> ==================================================================
> David A. Case                     |  e-mail:
> Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
> The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Tue Aug 06 2002 - 10:23:13 PDT
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