Subject: charm parameter in amber

From: Fujitsuka Yoshimi <[email-masked]>
Date: Wed, 27 Oct 1999 22:37:49 +0900 (JST)

Dear CCL,

  I'd like to use charm22 parameters in amber. Is it possible?
 If it's possible, are there any programs which convert charm22
 parameters to amber format files like 'parm94.dat'?

Thanks

     YOSHIMI FUJITSUKA
    Theoretical Chemistry Laboratory
    Department of Chemistry,Faculity of Science
    Nagoya Univercity
    Japan
    (e-mail)  [email-masked]

---

From: David Case <[email-masked]>
Date: Wed, 27 Oct 1999 09:21:05 -0700

>  parameters to amber format files like 'parm94.dat'?

We've got close to this, but never had the resources to really finish it
off, basically by having someone familiar enough with both CHARMM and Amber
to decide if things are really working.  If you want to give things a try,
you can look at the material in

    ftp://ftp.scripps.edu/pub/case/c22_in_amber.tar.gz

Equivalent (slightly updated) material will be a part of Amber 6, due out
soon.  But be warned: you will need to recompile Amber with special flags,
run some scripts to convert CHARMM files to Amber format (and then
hand-check the outputs).  You will also need access to CHARMM to decide
for yourself on the level of compatability you require.  Many CHARMM options
for handling long-range cutoffs are not implemented in Amber, although 
using PME for long-range electrostatics should be nearly the same in the two
codes.

We would love to have someone volunteer to complete this project!  (And,
of course, would give that person proper attribution on the resulting
files.)

....dac

-- 

==================================================================
David A. Case                     |  e-mail:      [email-masked]
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  WWW:                         
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================

---

From: "Jim Kress" <[email-masked]>
Date: Wed, 27 Oct 1999 14:16:16 -0400

You can do this with Tinker.

http://dasher.wustl.edu/tinker/

Jim

Check out my web site  http://www.kressworks.com/
It'll blow your mind (politically), stimulate your senses (artistically)
and provide scientific insights that boggle the mind!

----- Original Message -----
From: Fujitsuka Yoshimi <[email-masked]>
To: <[email-masked]>
Sent: Wednesday, October 27, 1999 9:37 AM
Subject: CCL:charm parameter in amber

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