Re: Amber tutorial crown-ether

From: David A. Case <>
Date: Tue 21 Jan 2003 08:48:47 -0800

On Tue, Jan 21, 2003, Dvira Segal wrote:
> I am trying to run Amber tutorial 'crown-ether' and unfortunately
> encounter many problems. I understand that it was written for older
> versions, but still I have some basic non-version related problems...
> 1) For example, the gibbs part ("Running the gibbs program" ) runs
> gibbs -O \
> -i \
> -p ../setup/ \
> -c ../dynamics/md0.rst \
> -o gib_na_k.out \
> -r gib_na_k.rst
> I dont see above where the coordinate file md0.rst was created.

Use an equilibrated file from the dynamics section, such as md_na.rst.

> 2) Same problem with the dynamics part which needs the files
> and crowni.crd - What are these files? I dont see them in the setup
> section.

Make this as for the perturbed prmtop files, but use saveAmberParm rather
than saveAmberParmPert.

> 3) Is there a newer version of this tutorial (Im using amber7)

No. Note that, for beginners, it is generally more straightforward to
use sander rather than gibbs to do free energy simulations. Set up the
pertrubed prmtop file as for gibbs, but then follow the instructions in
the Users' Manual, section 5.6.18. For this demo, you just set icfe=1,
and run a series of runs with different values of clambda. Then add up
the resulting estimates of <dV/dlambda> as indicated in the manual.

..good luck...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
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Jan 21 2003 - 08:48:47 PST
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