AMBER Archive (2009)

Subject: [AMBER] problem with antechamber

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Wed Apr 08 2009 - 01:32:32 CDT

Dear amber users,

                        I am working with some organic molecules. I am using
all the parameters from literature, compatible with amber. So using
antechamber I created the prep file . Some of the bonds in my molecule have
a length of about 1.8 A. When I am using parmchk for creating the frcmod
file , it didn't give any warning about the missing parameters of the bond
which are more than 1.8 A. When I tried reducing the bond length in the prep
file , say below 1.7 A, the frcmod file is generated with warnings about
all the parameters so that I can enter my parameters in the frcmod file. Can
anyone help me figure out this problem?

My frcmod given below

*******************************************************
*Before changing the bond length*
remark goes here
MASS
x1 0.000 0.000 ATTN, need revision
b 0.000 0.000 ATTN, need revision
x3 0.000 0.000 ATTN, need revision
x4 0.000 0.000 ATTN, need revision
x2 0.000 0.000 ATTN, need revision

BOND

ANGLE

DIHE

IMPROPER

NONBON
  x1 0.0000 0.0000 ATTN, need revision
  b 0.0000 0.0000 ATTN, need revision
  x3 0.0000 0.0000 ATTN, need revision
  x4 0.0000 0.0000 ATTN, need revision
  x2 0.0000 0.0000 ATTN, need revision
**********************************************************************
**********************************************************************
*After changing the bond length below 1.7A
*remark goes here
MASS
x1 0.000 0.000 ATTN, need revision
b 0.000 0.000 ATTN, need revision
x3 0.000 0.000 ATTN, need revision
x4 0.000 0.000 ATTN, need revision
x2 0.000 0.000 ATTN, need revision

BOND
x1-b 0.00 0.000 ATTN, need revision
b -x3 0.00 0.000 ATTN, need revision
b -x4 0.00 0.000 ATTN, need revision
b -x2 0.00 0.000 ATTN, need revision

ANGLE
x1-b -x3 0.000 0.000 ATTN, need revision
x1-b -x4 0.000 0.000 ATTN, need revision
x1-b -x2 0.000 0.000 ATTN, need revision
x3-b -x4 0.000 0.000 ATTN, need revision
x3-b -x2 0.000 0.000 ATTN, need revision
x4-b -x2 0.000 0.000 ATTN, need revision

DIHE

IMPROPER

NONBON
  x1 0.0000 0.0000 ATTN, need revision
  b 0.0000 0.0000 ATTN, need revision
  x3 0.0000 0.0000 ATTN, need revision
  x4 0.0000 0.0000 ATTN, need revision
  x2 0.0000 0.0000 ATTN, need revision
**********************************************************************
**********************************************************************

Thanks in advance
Aneesh

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