Running benzene example


Just Got Here
I am having problem with running the benzene example that comes with the nwchem6.6, below is the output of the run:

          Job information
---------------

   hostname        = node38
program = /home/projects/HPCMON/apps/nwchem-6.6/bin/LINUX64/nwchem
date = Fri Nov 3 21:05:12 2017

   compiled        = Sun_Oct_29_19:58:24_2017
source = /home/projects/HPCMON/apps/nwchem-6.6
nwchem branch = 6.6
nwchem revision = 27746
ga revision = 10594
input = benzene.nw
prefix = benzene.
data base = ./benzene.db
status = startup
nproc = 16
time left = -1s



          Memory information
------------------

   heap     =   13107200 doubles =    100.0 Mbytes
stack = 13107197 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428797 doubles = 400.0 Mbytes
verify = yes
hardfail = no


          Directory information
---------------------

 0 permanent = .
0 scratch = .




                               NWChem Input Module
-------------------


                                 Prepare Module
--------------

Force field


Directories used for fragment and segment files


Parameter files used to resolve force field parameters

PDB geometry                          benzene.pdb


Creating fragment for residue bnz


Fragment                              bnz

 num name  type   link cntr  grp pgrp    charge     polarizab

   1  C1             0    6    0    1    1    0.000000    0.000000
2 H1 0 0 0 1 1 0.000000 0.000000
3 C2 0 6 0 1 1 0.000000 0.000000
4 H2 0 0 0 1 1 0.000000 0.000000
5 C3 0 6 0 1 1 0.000000 0.000000
6 H3 0 0 0 1 1 0.000000 0.000000
7 C4 0 6 0 1 1 0.000000 0.000000
8 H4 0 0 0 1 1 0.000000 0.000000
9 C5 0 6 0 1 1 0.000000 0.000000
10 H5 0 0 0 1 1 0.000000 0.000000
11 C6 0 6 0 1 1 0.000000 0.000000
12 H6 0 0 0 1 1 0.000000 0.000000
------------
total charge 0.000000

Connectivity

      1-  2
1- 3
1- 11
3- 4
3- 5
5- 6
5- 7
7- 8
7- 9
9- 10
9- 11
11- 12

Created fragment                      bnz.frg_TMP

Unresolved atom types in fragment bnz


**********
* 0: pre_mkfrg failed 9999
**********
0::Received an Error in Communication


The bnz.frg_TMP:

  1. This is an automatically generated fragment file
  2. Atom types and connectivity were derived from coordinates
  3. Atomic partial charges are crude estimates
  4. 11/03/17 21:05:12

$bnz
  12    1    1    0
bnz
   1 C1             0    6    0    1    1    0.000000    0.000000
2 H1 0 0 0 1 1 0.000000 0.000000
3 C2 0 6 0 1 1 0.000000 0.000000
4 H2 0 0 0 1 1 0.000000 0.000000
5 C3 0 6 0 1 1 0.000000 0.000000
6 H3 0 0 0 1 1 0.000000 0.000000
7 C4 0 6 0 1 1 0.000000 0.000000
8 H4 0 0 0 1 1 0.000000 0.000000
9 C5 0 6 0 1 1 0.000000 0.000000
10 H5 0 0 0 1 1 0.000000 0.000000
11 C6 0 6 0 1 1 0.000000 0.000000
12 H6 0 0 0 1 1 0.000000 0.000000
1 2
1 3
1 11
3 4
3 5
5 6
5 7
7 8
7 9
9 10
9 11
11 12


The bnz.frg file:

  1. This is an automatically generated fragment file
  2. Atom types and connectivity were derived from coordinates
  3. Atomic partial charges are crude estimates
  4. 12/08/04 15:18:43

$bnz
  12    1    1    0
bnz
   1 C1   CA        0    1    0    1    1   -0.050000    0.000000
2 H1 HA 0 0 0 1 1 0.050000 0.000000
3 C2 CA 0 1 0 1 1 -0.050000 0.000000
4 H2 HA 0 0 0 1 1 0.050000 0.000000
5 C3 CA 0 1 0 1 1 -0.050000 0.000000
6 H3 HA 0 0 0 1 1 0.050000 0.000000
7 C4 CA 0 1 0 1 1 -0.050000 0.000000
8 H4 HA 0 0 0 1 1 0.050000 0.000000
9 C5 CA 0 1 0 1 1 -0.050000 0.000000
10 H5 HA 0 0 0 1 1 0.050000 0.000000
11 C6 CA 0 1 0 1 1 -0.050000 0.000000
12 H6 HA 0 0 0 1 1 0.050000 0.000000
1 2
1 3
1 11
3 4
3 5
5 6
5 7
7 8
7 9
9 10
9 11
11 12


Any idea?


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