AMBER Archive (2009)
Subject: [AMBER] rings getting planar

From: Jio M (jiomm_at_yahoo.com)
Date: Thu Nov 26 2009 - 03:33:09 CST

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Dear Amber users;

1 ) I have a molecule (as shown in attached file;; it is shown in non-relaxed position). the two rings should be
nearly perpendicular to each other and the same I got from Gaussian out
file. when saved it as mol2 file in AMBER and missing parameters were
added to it I got the following frcmod file (only part is shown)

cd-cd-os-ca   1
1.050
180.000
2.000      same as X -c2-os-X

cd-cc-ca-ca   1
2.550
180.000
2.000      same as X -c2-ca-X

cc-cd-os-ca   1
1.050
180.000
2.000      same as X -c2-os-X

ca-ca-cc-ca   1
2.550
180.000
2.000      same as X -c2-ca-X

when I relax molecule (in xleap gui interface)
this ( ca-ca-cc-ca and cd-cc-ca-ca) force two rings to be in same
plane {{{please correct me if I am wrong}}}. but they should not be.. what other force field I can use for
such problem..

2) For dynamics part,, If I use the same parameters for this molecule
and do sander minimization with restraints on solute,, output is
normal. But when restraints are removed 1-4 EEL and EAMBER is
shown as stars ( total energy has some value ) and no rst file is
obtained. Is it due fact that wrong parameters are being used here
which cause rings to get planar when restraints are removed

only starting steps shown (total 5000 steps)

NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

      1
3.7356E+03     4.3725E+00
6.5490E+01
H16       373

BOND    =
198.8658 ANGLE   =
3086.5268 DIHED
=      813.7483

VDWAALS =    -3359.2038
EEL     =     -927.2489
HBOND
=        0.0000

1-4 VDW =      552.5167 1-4 EEL
=     3370.3766 RESTRAINT
=        0.0000

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

     50
2.4504E+03     1.0554E+00
3.9612E+01     C13
1402

BOND    =
113.1459 ANGLE   =
1776.4162 DIHED
=      779.9294

VDWAALS =    -3527.9560
EEL     =     -943.4331
HBOND
=        0.0000

1-4 VDW =      469.0179 1-4 EEL
=     3173.3223 RESTRAINT
=      609.9626

EAMBER = 1840.4426

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    100
2.3883E+03     1.4690E+00
7.8804E+01
N1       1380

BOND    =
116.3442 ANGLE   =
1621.6861 DIHED
=      776.1233

VDWAALS =    -3537.7520
EEL     =     -940.2036
HBOND
=        0.0000

1-4 VDW =      462.7917 1-4 EEL
=     3155.3384 RESTRAINT
=      733.9614

EAMBER = 1654.3280

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    150
7.8116E+02     3.0855E+02
2.1150E+04
O4       1491

BOND    =
163.6658 ANGLE   =
1654.8874 DIHED
=      773.9477

VDWAALS =    -3535.5676
EEL     =     -935.1865
HBOND
=        0.0000

1-4 VDW =      461.8045 1-4 EEL
=     1381.5643 RESTRAINT
=      816.0479

EAMBER = -34.8845

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    200
-1.8594E+08     3.0912E+12
2.1224E+14
O4       1491

BOND    =
170.6509 ANGLE   =
1662.4294 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0846

EAMBER = *************

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    250
-3.0972E+08     8.5765E+12
5.8887E+14
O4       1491

BOND    =
170.6510 ANGLE   =
1662.4294 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0846

EAMBER = *************

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    300
-5.8711E+07     3.0821E+11
2.1162E+13
O4       1491

BOND    =
170.6508 ANGLE   =
1662.4292 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0845

EAMBER = *************

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    350
-1.7161E+08     2.6332E+12
1.8080E+14
O4       1491

BOND    =
170.6509 ANGLE   =
1662.4294 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0846

EAMBER = *************

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    400
-3.0972E+08     8.5765E+12
5.8887E+14
O4       1491

BOND    =
170.6510 ANGLE   =
1662.4294 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0846

EAMBER = *************

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    450
-5.8711E+07     3.0821E+11
2.1162E+13
O4       1491

BOND    =
170.6508 ANGLE   =
1662.4292 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0845

EAMBER = *************

   NSTEP
ENERGY
RMS
GMAX
NAME    NUMBER

    500
-1.7161E+08     2.6332E+12
1.8080E+14
O4       1491

BOND    =
170.6509 ANGLE   =
1662.4294 DIHED
=      774.1576

VDWAALS =    -3535.5512
EEL     =     -934.9079
HBOND
=        0.0000

1-4 VDW = 461.8032 1-4 EEL =
************* RESTRAINT =
819.0846

EAMBER = *************

please suggest;

thanks and regards;

JIomm

image/png attachment: Screenshot.png

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