Date: Thu, 26 Nov 2009 01:33:09 -0800 (PST)
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
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