AMBER Archive (2003)

Subject: Re: AMBER: "ATTN, need revision"

From: Junmei Wang (JWang_at_encysive.com)
Date: Thu Aug 28 2003 - 12:06:46 CDT

Hi, Anne,

"ATTN, need revision" means parmchk cannot suggest a reasonable parameter
and need users' intervention. For this specific case, the bond angle should
be 180 and force constant may be set to 56.9 as c1-c1-ca has. Actually, the
bond angle force constants in AMBER are pretty crude.

For the new version of gaff (in amber8), we have introduced more atom types
and parameters. This kinds of problem ("ATTN, need revision") is much fewer
if not extinct.

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

                                                                           
             <atobak_at_eden.rutg
             ers.edu>
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             ps.edu cc
                                                                           
                                                                   Subject
             08/28/2003 11:31 AMBER: "ATTN, need revision"
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

I have a question about some of the gaff.dat parameters included in my
frcmod file. For the ca-c1-n1 angle, the parameters are zero and the
included message is "ATTN, need revision":

*************************************************************
remark goes here
MASS

BOND

ANGLE
f -c3-ca 64.122 109.730 Calculated with empirical approach
ca-c1-n1 0.000 0.000 ATTN, need revision
c -c3-oh 66.939 111.330 Calculated with empirical approach

DIHE

IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 Using
default value
c1-ca-ca-ca 1.1 180.0 2.0 Using
default value
ca-ca-ca-n 1.1 180.0 2.0 Using
default value

NONBON

************************************************************

I understand that I need to manually edit this file to correct this
problem before reading it into LEAP, but I am unsure of what values to
insert into the 2 parameter columns. The ca-c1-n1 angle is a carbon1
bonded to another carbon which is then triple bonded to a nitrogen. The
angle structure is linear. Therefore, shouldn't the parameter value be
180 instead of 0? What values should I insert in the two columnns?

Also, in the Amber manual, it states that the gaff.dat file is
continuously updated. Where can I find this updated file?

Thank you very much,

Anne Tobak

P.S. I'm using Amber version 7 on a Linux Dell machine

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