AMBER Archive (2003)

Subject: Nmanal

From: Gus Carri (carri_at_charles.polymer.uakron.edu)
Date: Wed Jul 02 2003 - 16:26:50 CDT

        Hello all. I am having the following problem with Nmanal. This is
how I put it to run.

nmanal -O -i nmanal.in -o nmanal.out -p eth-2.top -v nmode.vec

where nmode.vec is created by nmode. eth-2.top was created from the prmtop
file that xleap created using new2oldparm < eth.top > eth-2.top. This is
nmanal.in

Normal modes for CH2=CH2
&data
 ntrun = 1 ,
 nvect = 18 ,
 ipro = 1 ,
 ivform = 0 ,
 ibeg = 1 ,
 iend = 18 ,
 ifluc = 1 ,
&end

This is the complain from nmanal

nmanal -O -i nmanal.in -o nmanal.out -p eth-2.top -v nmode.vec
fmt: read unexpected character
apparent state: unit 20 named eth-2.top
last format: (5E16.8)
lately reading sequential formatted external IO
Aborted

This is the nmode.vec file

more nmode.vec
NORMAL COORDINATE FILE
   18
    3.30799 2.33203 1.90901 3.83759 1.39110 1.86518
3.87029
    3.25365 1.95565 1.98698 2.35538 1.90562 1.45737
3.29631
    1.94945 1.42467 1.43376 1.85899
 ****
    1 0.00000
   -0.07430 -0.12586 -0.11952 -0.07430 -0.12586 -0.11952
-0.07430
   -0.12586 -0.11952 -0.07430 -0.12586 -0.11952 -0.07430
-0.12586
   -0.11952 -0.07430 -0.12586 -0.11952
 ****
    2 0.00000
    0.07002 -0.14070 0.10463 0.07002 -0.14070 0.10463
0.07002
   -0.14070 0.10463 0.07002 -0.14070 0.10464 0.07002
-0.14070
    0.10464 0.07002 -0.14070 0.10464
 ****
    3 0.00002
    0.15882 0.00315 -0.10205 0.15882 0.00315 -0.10205
0.15882
    0.00315 -0.10205 0.15882 0.00315 -0.10205 0.15882
0.00315
   -0.10205 0.15882 0.00315 -0.10205
 ****
    4 0.00932
   -0.00056 -0.00792 0.16317 -0.00101 -0.01434 0.29562
-0.00103
   -0.01457 0.30045 0.00056 0.00791 -0.16316 0.00101
0.01434
   -0.29562 0.00103 0.01457 -0.30045
 ****
    5 0.01256
   -0.00260 -0.14804 -0.00719 -0.21397 -0.26671 -0.01367
0.20447
   -0.27411 -0.01260 0.00260 0.14804 0.00719 0.21397
0.26671
    0.01367 -0.20447 0.27411 0.01260
 ****
    6 0.02210
    0.00000 -0.00004 0.00079 -0.00171 -0.02420 0.49886
0.00170
    0.02406 -0.49597 0.00000 0.00004 -0.00079 0.00171
0.02420
   -0.49887 -0.00170 -0.02406 0.49597
 ****
    7 907.48550
    0.00026 0.00375 -0.07726 -0.00158 -0.02233 0.46029
-0.00158
   -0.02233 0.46029 0.00026 0.00375 -0.07726 -0.00158
-0.02233
    0.46029 -0.00158 -0.02233 0.46029
 ****
    8 1043.57202
   -0.00042 -0.00592 0.12211 0.00136 0.01932 -0.39825
0.00136
    0.01932 -0.39825 0.00042 0.00592 -0.12211 -0.00136
-0.01932
    0.39825 -0.00136 -0.01932 0.39825
 ****
    9 1044.16722
    0.00064 0.03637 0.00177 -0.44311 -0.20889 -0.01165
0.43550
   -0.22442 -0.00939 0.00064 0.03637 0.00177 -0.44311
-0.20889
   -0.01165 0.43550 -0.22442 -0.00939
 ****
   10 1194.27259
    0.00000 0.00000 0.00000 -0.00170 -0.02413 0.49742
0.00170
    0.02413 -0.49742 0.00000 0.00000 0.00000 -0.00170
-0.02413
    0.49742 0.00170 0.02413 -0.49742
 ****
   11 1293.35360
   -0.00209 -0.11892 -0.00578 0.39729 0.07532 0.00501
-0.39440
    0.08932 0.00298 0.00209 0.11892 0.00578 -0.39729
-0.07532
   -0.00501 0.39440 -0.08932 -0.00298
 ****
   12 1298.81728
    0.14204 -0.00251 0.00036 0.34530 0.09230 0.00566
0.34185
   -0.10445 -0.00390 -0.14204 0.00251 -0.00036 -0.34530
-0.09230
   -0.00566 -0.34185 0.10445 0.00390
 ****
   13 1681.94992
   -0.06399 0.00113 -0.00016 0.38611 0.27262 0.01455
0.37630
   -0.28610 -0.01259 -0.06399 0.00113 -0.00016 0.38611
0.27262
    0.01455 0.37630 -0.28610 -0.01259
 ****
   14 1840.99222
   -0.13404 0.00237 -0.00034 0.25475 0.27539 0.01423
0.24492
   -0.28423 -0.01295 0.13404 -0.00237 0.00034 -0.25475
-0.27539
   -0.01423 -0.24492 0.28423 0.01295
 ****
   15 2943.27403
    0.04344 -0.00077 0.00011 -0.25158 0.41605 0.01932
-0.26603
   -0.40690 -0.02065 0.04344 -0.00077 0.00011 -0.25158
0.41605
    0.01932 -0.26603 -0.40690 -0.02065
 ****
   16 2971.72528
    0.05895 -0.00104 0.00015 -0.25275 0.40382 0.01872
-0.26677
   -0.39464 -0.02006 -0.05895 0.00104 -0.00015 0.25275
-0.40382
   -0.01872 0.26677 0.39464 0.02006
 ****
   17 3057.73955
   -0.00120 -0.06816 -0.00331 -0.22728 0.41018 0.01912
0.24154
    0.40189 0.02032 -0.00120 -0.06816 -0.00331 -0.22728
0.41018
    0.01912 0.24154 0.40189 0.02032
 ****
   18 3071.66348
    0.00130 0.07390 0.00359 0.21070 -0.41307 -0.01932
-0.22507
   -0.40536 -0.02043 -0.00130 -0.07390 -0.00359 -0.21070
0.41307
    0.01932 0.22507 0.40536 0.02043

This is eth-2.top

more eth-2.top
eth
     6 2 4 1 6 0 4 0 0 0 16 1
     1 0 0 2 2 1 2 0 0 0 0 0
     0 0 0 1 6 0 0
C1 H3 H4 C2 H5 H6
 -3.97246140E+00 1.98623070E+00 1.98623070E+00 -3.97246140E+00
1.98623070E+00
  1.98623070E+00
  1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.00800000E+00
  1.00800000E+00
     1 2 2 1 2 2
     5 4 3 2 1 1
     1 2 2 3
eth
     1
  3.54500000E+02 5.97700000E+02
  1.08000000E+00 1.32000000E+00
  5.00000000E+01 3.81000000E+01
  2.08916001E+00 2.07554644E+00
  6.65000000E+00
  2.00000000E+00
  3.14159400E+00
  0.00000000E+00 0.00000000E+00
  8.19971662E+05 8.61541883E+04 7.51607703E+03
  5.31102864E+02 1.12529845E+02 2.17257828E+01
     0 3 1 0 6 1 9 12 1 9 15 1
     0 9 2
     0 9 12 1 0 9 15 1 3 0 6 2
     3 0 9 1 6 0 9 1 12 9 15 2

     3 0 9 12 1 3 0 9 15 1 6 0
     9 12 1 6 0 9 15 1

     2 3 4 5 6 3 4 5 6 4 5 6
     5 6 6 0

c2 hc hc c2 hc hc
M E E M E E
     0 0 0 0 0 0
     0 0 0 0 0 0
     1 1 2
     6
  9.00000000E+01 5.29482746E+00 4.68594027E+00 3.81600165E+00

Any suggetions ?

                        Gus