AMBER Archive (2003)

Subject: Re: AMBER: PARMSET problem

From: Junmei Wang (JWang_at_encysive.com)
Date: Wed Aug 20 2003 - 13:06:00 CDT

I would like to suggest you assign hydrogen in H-C=C to HA. Then CM-HA,
CM-CM-HA are available. CT-CM-HA is still missing for parm94 and parm99,
you may use parameter of c3-c2-ha (45.9 117.3) in gaff instead.

Regards

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
===============================================================

                                                                           
             "Yichen Cao"
             <ycao0_at_uky.edu>
             Sent by: To
             owner-amber_at_scrip amber_at_scripps.edu
             ps.edu cc
                                                                           
                                                                   Subject
             08/20/2003 12:07 AMBER: PARMSET problem
             PM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

Dear Amber users:

I got a problem when I created the .top and .crd files for 1,9 decadiene
molecule. I assigned the 'CM' to carbon atom of the C=C double bond and
'HC' for all the hydrogens in the molecule. However when I tried to
generate .top and .crd files, the xleap reported that it could not find the
'bond' and 'angle' parameters for CM-HC, CM-CM-HC, CT-CM-HC, etc. My
questions are:

1. Did I assign the atom type wrong to the Carbon and hydrogen atoms?
2. What PARAMSETS should I use for 1,9-decadiene?

Thanks,
Yichen

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