CCL: using TINKER

[Jakob Petersen <petersen.jakob---gmail.com>]

 Dear Jonas,

I'm using the TINKER package for windows (running with
 FFE) and linux (running with shell script), and during the last 5 months I have
 been looking for a mailing list too. Now my calculations are running fine, but
 writing the .xyz and .key files (and making it all work) was a tedious job.
 Mostly, I'm using TINKER for molecular dynamics simulations, but I guess,
 that some of the "problems" I have encountered is universal for
 TINKER. If you have a specific question, let me know - maybe I can help you
 out.
 
Greetings,
Jakob

On Fri, Nov 6, 2009 at 5:06 AM, A VM fray.gory###gmail.com <owner-chemistry]_[ccl.net> wrote:

Dear Jonas,

For linux...

To me the greatest trick resides in defining correctly the PATH variable
in the shell that you are using.
(I mean, in my case, PATH=/opt/MolecularStructure/tinker/bin:$PATH)

Also, as I work is generating the coordinates files with MOLDEN, and 
assigning carefully the parameters with the 'FF' in the control window,
see MOLDEN web page, and saving them as TINKER xyz.

Hope that it helps (at least a little bit).

Alvaro



Alvaro Vazquez-Mayagoitia

On Thu, Nov 5, 2009 at 8:36 PM, Jonas Baltrusaitis jasius_1||yahoo.com <owner-chemistry*ccl.net> wrote:

Sent to CCL by: "Jonas  Baltrusaitis" [jasius_1_-_yahoo.com]
Dear all,

is anybody using TINKER by any chance? I have been trying to run jobs using FFE but found it impossible. Manual is to concise and I can;t run any jobs as I find pdbxyz, nucleic and protein commands only, whereas in the manual it clearly shows Optimize, no idea how to get there.

is there any mailing list or board for Tinker?

thanks

Jonas



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