AMBER Archive (2003)

Subject: Re: AMBER: cd-c-os and c3-cd-c angle parameters

From: Junmei Wang (JWang_at_encysive.com)
Date: Wed Sep 24 2003 - 13:16:18 CDT

The machine of sigyn at ucsf has been shut down and antechamber website is
temporarily not available. It will be linked to amber homepage some days
later. For your parameters, I have found them in the latest gaff.dat
file,
cd-c -os 70.5 (force constant) 112.30 (equilibrium angle) 6
(number of occurrence in test set) 2.3802 (deviation)
c -cd-c3 64.9 (force constant) 112.75 (equilibrium angle) 4
(number of occurrence in test set) 0.2063 (deviation)

Best

Junmei
===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             "Vikas Varshney"
             <vikas_var_at_rediff
             mail.com> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       AMBER: cd-c-os and c3-cd-c angle
             09/24/2003 10:10 parameters
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

Hi,
I am having some problem in getting cd-c-os and c3-cd-c angle
parameters as they
are not defined in the gaff.dat file. At the end of the file it is
written that

Please find the latest parameter file from
  www.amber.ucsf.edu/antechamber.html

I looked at this URL, but it didn't open. My molecule is methyl
methacrylate.

I will really appreciate if any of you can help me in getting
these parameters either by
giving me the updated link of this site where latest gaff.dat file
is present or some
other way of getting these parameters.

Regards,
Vikas

On Wed, 24 Sep 2003 Robert Duke wrote :
>Dear Amber users,
>The latest update of PMEMD (3.03) is now available at the Amber
>web page,
>amber.scripps.edu. This update has the following features:
>1) The Amber 7 parameter-topology file (prmtop) format is now
>supported.
>This allows one to directly use prmtop files created by Amber 7
>leap, and
>basically provides support for large problems. The amber 6
>format prmtop is
>limited in that it will only support 33,332 atoms with dihedral
>information.
>I have tested PMEMD with a system of about 540,000 atoms and a
>system with
>more than 33,332 dihedrals, and it works.
>2) A bugfix for a problem reported earlier on the Amber reflector
>with COM
>velocity removal. This is the only critical bugfix in 3.03.
>3) A minor bugfix for a segmentation fault when iwrap .gt. 0 and
>ntwprt .gt.
>0.
>
>A more detailed description is given in the 3.03 update notice
>available at
>amber.scripps.edu.
>
>Regards - Bob Duke
>
>
>
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