AMBER Archive (2002)

Subject: Re: creating a solvent box

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 06 2002 - 13:53:50 CDT

On Tue, Aug 06, 2002, Bimo Ario Tejo wrote:
>
> I have problem when creating a CCl4 solvent box. I have equilibrated the
> solvent and got ccl4box.xyz file. I converted it into ccl4box.pdb file using
> ambpdb (with new2oldparams). Up to this stage I have no problem

(I'm a little confused here, since ambpdb knows about new parameter files;
it doesn't require new2oldparams....)

>
> 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?
>

First, it would help a lot if you gave the actual error message (and how
you got there). Just writing "xleap said there's no parameters for my solvent
box" is not really specific enough. Also, giving the commands you actually
entered (rather than just "check its geometry") would also help.

Second, I'm guessing(?) that you did not re-load the frcmod.ccl4 file along
with the ccl4box.lib the final time you ran xleap (when you got the error).
Parameters are not stored inside .lib files--you need to load them every time
you run leap.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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