Trying to set up a small test with some non-standard atoms in my parameter file and the non-standard atoms are not being recognized. The atoms are Al but are typed AO in the forcefield I am using. Can anyone help me determine the problem?
Thanks
The input file is:
start rwh
permanent_dir ./
scratch_dir ./
prepare
source rwh.pdb
new_top new_seq
new_rst
modify segment 1 quantum
update lists
ignore
write rwh_ref.pdb
write rwh_ref.rst
end
task prepare
The amber.par file in my working directory is
CLAYFF 99 CUSTOM PARAMETERS
Electrostatic 1-4 Scaling Factor 1.00
Relative dielectric constant 1.000000
Parameters epsilon R*
Atoms
AO 26.98154 5.56388E-06 0.23972 1 1111111111
13 5.56388E-06 0.23972
FE 55.84500 3.77807E-06 0.27535 1 1111111111
26 3.77807E-06 0.27535
H 1.00800 0 0.17766 1 1111111111
1 0 0.17766
HO 1.00800 0 0.17766 1 1111111111
1 0 0.17766
O 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
OH 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
OB 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
OBOS 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
OBTS 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
OBSS 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
OHS 15.99940 0.65019 0.17766 1 1111111111
8 0.65019 0.17766
ST 28.08550 7.70065E-06 0.18532 1 1111111111
8 7.70065E-06 0.18532
AT 26.98154 7.70065E-06 0.18532 1 1111111111
13 7.70065E-06 0.18532
MGO 24.30500 3.77807E-06 0.29545 1 1111111111
12 3.77807E-06 0.29545
MGH 24.30500 3.77807E-06 0.29545 1 1111111111
12 3.77807E-06 0.29545
NA 22.98977 0.5443384 0.13189 1 1111111111
11 0.5443384 0.13189
CG 12.01100 0.292880 0.19924 1 1111111111
6 0.292880 0.19924
HG 1.00800 0.125520 0.13582 1 1111111111
1 0.125520 0.13582
OG 15.99940 0.803746 0.17650 1 1111111111
8 0.803746 0.17650
HP 1.00800 0.192464 0.02245 1 1111111111
1 0.192464 0.02245
FE 55.84500 3.77808E-06 0.27535 1 1111111111
26 3.77808E-06 0.27535
Bonds
O -H 0.10000 0.46370e+06
OH -HO 0.10000 0.46370e+06
OHS -HO 0.10000 0.46370e+06
CG -HG 0.10800 0.28451e+06
CG -OG 0.14110 0.27974e+06
CG -CG 0.13750 0.25524e+06
OG -HP 0.09600 0.45606e+06
Angles
H -O -H 1.91061 3.83000e+02
ST -OH -HO 1.91061 2.51040e+02
ST -OHS -HO 1.91061 2.51040e+02
AO -OH -HO 1.91061 2.51040e+02
AO -OHS -HO 1.91061 2.51040e+02
AT -OH -HO 1.91061 2.51040e+02
AT -OHS -HO 1.91061 2.51040e+02
MGO -OH -HO 1.91061 2.51040e+02
MGO -OHS -HO 1.91061 2.51040e+02
MGH -OH -HO 1.91061 2.51040e+02
MGH -OHS -HO 1.91061 2.51040e+02
CG -CG -CG 2.09440 3.34720e+02
CG -CG -HG 2.09440 2.51040e+02
CG -CG -OG 2.09440 3.78234e+02
CG -OG -HP 1.88496 5.43920e+02
Proper dihedrals
OG -CG -CG -OG 3.14159 10.79472 2
CG -CG -CG -CG 3.14159 12.97040 2
CG -CG -CG -HG 3.14159 17.5728 2
CG -CG -CG -OG 3.14159 12.9704 2
CG -CG -OG -HP 3.14159 4.14216 2
HG -CG -CG -HG 3.14159 10.0416 2
OG -CG -CG -HG 3.14159 10.0416 2
Improper dihedrals
CG -CG -CG -HG 3.14159 17.5728 2
CG -CG -CG -OG 3.14159 12.9704 2
CG -CG -CG -CG 3.14159 12.97040 2
and the output is
argument 1 = rwh.nw
Northwest Computational Chemistry Package (NWChem) 6.8
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2017
Pacific Northwest National Laboratory
Battelle Memorial Institute
NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file
ACKNOWLEDGMENT
--------------
This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.
Job information
---------------
hostname = ccmm4
program = nwchem
date = Wed May 15 16:04:55 2019
compiled = Wed_Jan_30_11:39:26_2019
source = /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8
nwchem branch = 6.8
nwchem revision = v6.8-47-gdf6c956
ga revision = ga-5.6.3
use scalapack = F
input = rwh.nw
prefix = rwh.
data base = .//rwh.db
status = startup
nproc = 2
time left = -1s
Memory information
------------------
heap = 13107194 doubles = 100.0 Mbytes
stack = 13107199 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428793 doubles = 400.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = ./
0 scratch = ./
NWChem Input Module
-------------------
Prepare Module
--------------
Force field amber
Directories used for fragment and segment files
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_s/
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_q/
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_x/
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_u/
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_c/
./
Parameter files used to resolve force field parameters
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_s/amber.par
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_q/amber.par
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_x/amber.par
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_u/amber.par
/home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_c/amber.par
./amber.par
PDB geometry rwh.pdb
Creating fragment for residue PNO
Atom type definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_s/amber.par
Atom type definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_q/amber.par
Atom type definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_x/amber.par
Atom type definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_u/amber.par
Bond charge definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_s/amber.par
Bond charge definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_q/amber.par
Bond charge definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_x/amber.par
Bond charge definitions /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_u/amber.par
Bond charge definitions ./amber.par
Fragment PNO
num name type link cntr grp pgrp charge polarizab
1 1C CA 0 6 0 1 1 -0.050000 0.000000
2 2C CA 0 6 0 1 1 -0.050000 0.000000
3 3C CA 0 6 0 1 1 -0.050000 0.000000
4 4C C 0 6 0 1 1 0.000000 0.000000
5 5C CA 0 6 0 1 1 -0.050000 0.000000
6 6C CA 0 6 0 1 1 -0.050000 0.000000
7 1H HA 0 0 0 1 1 0.050000 0.000000
8 2H HA 0 0 0 1 1 0.050000 0.000000
9 3H HA 0 0 0 1 1 0.050000 0.000000
10 4H HA 0 0 0 1 1 0.050000 0.000000
11 5H HA 0 0 0 1 1 0.050000 0.000000
12 1O 0 0 0 1 1 0.000000 0.000000
13 1FE 0 0 0 1 1 0.000000 0.000000
------------
total charge -0.000000
Connectivity
1- 2
1- 6
1- 7
2- 3
1- 2
1- 6
1- 7
2- 3
2- 8
3- 4
3- 9
4- 5
4- 12
5- 6
5- 10
6- 11
Created fragment ./PNO.frg_TMP
Unresolved atom types in fragment PNO
**********
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