AMBER Archive (2003)

Subject: AMBER: "ATTN, need revision"

From: atobak_at_eden.rutgers.edu
Date: Thu Aug 28 2003 - 11:31:05 CDT

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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