I am preparing a calculation for phenol (quantum) in a model for a clay. At the moment trying to get the prepare for just the phenol to complete successfully. The phenol frag file has been generated by manually adding the atom types for my phenol force field to the PNO.frg_TMP file that perpare created and then renaming the file to PNO.frg. I have an amber.par in my working directory that appears in the nwchem output, but I am getting an error that the first atom type, CG2R61, is not found. Any help would be appreciated.
The nwchem input file is;
start clay
permanent_dir ./
scratch_dir ./
prepare
source clay.pdb
new_top new_seq
new_rst
- modify atom 1:1CG quantum
- modify atom 1:2H1 quantum
- modify atom 1:3H1 quantum
- modify atom 1:4H1 quantum
update lists
ignore
write clay_ref.rst
write clay_ref.pdb
end
task prepare
The PNO.frg file is
- This is an automatically generated fragment file
- Atom types and connectivity were derived from coordinates
- Atomic partial charges are crude estimates
- 04/09/19 07:11:26
$PNO
13 1 1 0
PNO
11CG CG2R61 0 6 0 1 1 -0.115000 0.000000
22CG CG2R61 0 6 0 1 1 -0.113000 0.000000
33CG CG2R61 0 6 0 1 1 -0.116000 0.000000
44CG CG2R61 0 6 0 1 1 -0.108000 0.000000
55CG CG2R61 0 6 0 1 1 -0.116000 0.000000
66CG CG2R61 0 6 0 1 1 -0.113000 0.000000
71HG HGR61 0 0 0 1 1 0.115000 0.000000
82HG HGR61 0 0 0 1 1 0.115000 0.000000
93HG HGR61 0 0 0 1 1 0.115000 0.000000
104HG HGR61 0 0 0 1 1 0.115000 0.000000
115HG HGR61 0 0 0 1 1 0.115000 0.000000
121OG OG311 0 0 0 1 1 -0.530000 0.000000
131HP HGP1 0 0 0 1 1 0.420000 0.000000
1 2
1 6
1 7
2 3
2 8
3 4
3 9
4 5
4 12
5 6
5 10
6 11
12 13
The clay.pdb is
ATOM 1 1CG PNO 1 -21.193 21.631 4.340 1.00 0.00 C
ATOM 2 2CG PNO 1 -19.984 22.333 4.340 1.00 0.00 C
ATOM 3 3CG PNO 1 -19.981 23.730 4.340 1.00 0.00 C
ATOM 4 4CG PNO 1 -21.193 24.429 4.340 1.00 0.00 C
ATOM 5 5CG PNO 1 -22.405 23.731 4.340 1.00 0.00 C
ATOM 6 6CG PNO 1 -22.402 22.333 4.340 1.00 0.00 C
ATOM 7 1HG PNO 1 -21.193 20.539 4.340 1.00 0.00 H
ATOM 8 2HG PNO 1 -19.036 21.791 4.340 1.00 0.00 H
ATOM 9 3HG PNO 1 -19.048 24.296 4.340 1.00 0.00 H
ATOM 10 4HG PNO 1 -23.338 24.296 4.340 1.00 0.00 H
ATOM 11 5HG PNO 1 -23.350 21.791 4.340 1.00 0.00 H
ATOM 12 1OG PNO 1 -21.192 25.815 4.340 1.00 0.00 O
ATOM 13 !HP PNO 1 -21.192 26.815 4.340 1.00 0.00 O
END
and the amber.par file (first part) is
- CLAYFF CUSTOM PARAMETERS
Electrostatic 1-4 Scaling Factor 1.00
Relative dielectric constant 1.000000
Parameters epsilon R*
Atoms
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
AO 26.98154 5.56388E-06 0.23972 1 1111111111
13 5.56388E-06 0.23972
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
FE 55.84500 3.77807E-06 0.27535 1 1111111111
Q 26 3.77807E-06 0.27535
CG2R61 12.01100 0.292880 0.19924 1 1111111111
Q 6 0.292880 0.19924
HGR61 1.00800 0.125520 0.13582 1 1111111111
Q 1 0.125520 0.13582
OG311 15.99940 0.803746 0.17650 1 1111111111
Q 16 0.803746 0.17650
HGP1 1.00800 0.192464 0.02245 1 1111111111
Q 1 0.192464 0.02245
The output (first part) is
nwchem clay.nw
argument 1 = clay.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 = Tue Apr 9 07:47:08 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 = clay.nw
prefix = clay.
data base = .//clay.db
status = startup
nproc = 1
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 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/
./
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
./amber.par
Deleted existing sequence ./clay.seq
PDB geometry clay.pdb
Created sequence ./clay.seq
Parameter file /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_s/amber.par
Parameter file /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_q/amber.par
Parameter file /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_x/amber.par
Parameter file /home/rhall/NWCHEM_DISTRIBUTION/nwchem-6.8/src/data/amber_u/amber.par
Parameter file ./amber.par
Undetermined force field parameters
Parameters could not be found for atom type CG2R61
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