Hello, I have a task to create a polymer chain from a monomer link structure in a PDB. I enter the import command. And the error comes out:
Info: field = {mode → apply, style → none, error → true, debug → false,
check → {atomistic → true, charge → true}}
Info: applying ‘~/Загрузки/emc/v9.4.4/field/pcff/pcff.frc’
Warning: no rule found for {group, site} = {mol, 0}.
Error: core/fields.c:433 FieldsApply:
Missing rules.
Program aborted.
What could be the reason?
File polymer.esh:
ITEM OPTIONS
replace true
field pcff
density 0.85
ntotal
ITEM END
ITEM CLUSTERS
molecule import, name=“test”, type=structure, mode=pdb
ITEM END
File test.pdb:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.90
CRYST1 10.334 10.334 10.334 90.00 90.00 90.00 P 1 1
ATOM 1 H1 mol A 1 -0.016 -0.206 -5.819 1.00 0.00 mol H
ATOM 2 C2 mol A 1 -0.665 -2.130 3.842 1.00 0.00 mol C
ATOM 3 C3 mol A 1 -0.259 -0.689 3.518 1.00 0.00 mol C
ATOM 4 O4 mol A 1 -0.207 -0.528 2.111 1.00 0.00 mol O
ATOM 5 C5 mol A 1 0.169 0.658 1.594 1.00 0.00 mol C
ATOM 6 O6 mol A 1 0.471 1.634 2.284 1.00 0.00 mol O
ATOM 7 C7 mol A 1 0.188 0.664 0.102 1.00 0.00 mol C
ATOM 8 C8 mol A 1 -0.193 -0.469 -0.656 1.00 0.00 mol C
ATOM 9 C9 mol A 1 -0.160 -0.433 -2.064 1.00 0.00 mol C
ATOM 10 C10 mol A 1 0.255 0.735 -2.744 1.00 0.00 mol C
ATOM 11 C11 mol A 1 0.633 1.866 -1.988 1.00 0.00 mol C
ATOM 12 C12 mol A 1 0.599 1.831 -0.579 1.00 0.00 mol C
ATOM 13 C13 mol A 1 0.299 0.788 -4.246 1.00 0.00 mol C
ATOM 14 O14 mol A 1 0.657 1.787 -4.864 1.00 0.00 mol O
ATOM 15 O15 mol A 1 -0.086 -0.354 -4.873 1.00 0.00 mol O
ATOM 16 H16 mol A 1 -1.647 -2.362 3.431 1.00 0.00 mol H
ATOM 17 H17 mol A 1 0.716 -0.466 3.953 1.00 0.00 mol H
ATOM 18 H18 mol A 1 -0.978 0.011 3.945 1.00 0.00 mol H
ATOM 19 H19 mol A 1 -0.515 -1.378 -0.167 1.00 0.00 mol H
ATOM 20 H20 mol A 1 -0.456 -1.313 -2.617 1.00 0.00 mol H
ATOM 21 H21 mol A 1 0.954 2.770 -2.488 1.00 0.00 mol H
ATOM 22 H22 mol A 1 0.895 2.709 -0.022 1.00 0.00 mol H
ATOM 23 H23 mol A 1 0.050 -2.841 3.427 1.00 0.00 mol H
CONECT 1 15
CONECT 2 23 16 3
CONECT 3 4 2 18 17
CONECT 4 5 3
CONECT 5 7 4 6
CONECT 6 5
CONECT 7 8 12 5
CONECT 8 9 19 7
CONECT 9 10 20 8
CONECT 10 13 9 11
CONECT 11 10 21 12
CONECT 12 11 22 7
CONECT 13 15 14 10
CONECT 14 13
CONECT 15 1 13
CONECT 16 2
CONECT 17 3
CONECT 18 3
CONECT 19 8
CONECT 20 9
CONECT 21 11
CONECT 22 12
CONECT 23 2
MASTER 0 0 0 0 0 0 0 0 23 0 23 0
END
File test.psf
PSF
1 !NTITLE
REMARKS VMD-generated NAMD/X-Plor PSF structure file
23 !NATOM
1 mol 1 mol H1 H1 0.000000 1.0080 0
2 mol 1 mol C2 C2 0.000000 12.0110 0
3 mol 1 mol C3 C3 0.000000 12.0110 0
4 mol 1 mol O4 O4 0.000000 15.9990 0
5 mol 1 mol C5 C5 0.000000 12.0110 0
6 mol 1 mol O6 O6 0.000000 15.9990 0
7 mol 1 mol C7 C7 0.000000 12.0110 0
8 mol 1 mol C8 C8 0.000000 12.0110 0
9 mol 1 mol C9 C9 0.000000 12.0110 0
10 mol 1 mol C10 C10 0.000000 12.0110 0
11 mol 1 mol C11 C11 0.000000 12.0110 0
12 mol 1 mol C12 C12 0.000000 12.0110 0
13 mol 1 mol C13 C13 0.000000 12.0110 0
14 mol 1 mol O14 O14 0.000000 15.9990 0
15 mol 1 mol O15 O15 0.000000 15.9990 0
16 mol 1 mol H16 H16 0.000000 1.0080 0
17 mol 1 mol H17 H17 0.000000 1.0080 0
18 mol 1 mol H18 H18 0.000000 1.0080 0
19 mol 1 mol H19 H19 0.000000 1.0080 0
20 mol 1 mol H20 H20 0.000000 1.0080 0
21 mol 1 mol H21 H21 0.000000 1.0080 0
22 mol 1 mol H22 H22 0.000000 1.0080 0
23 mol 1 mol H23 H23 0.000000 1.0080 0
23 !NBOND: bonds
1 15 2 23 2 16 2 3
3 4 3 18 3 17 4 5
5 7 5 6 7 8 7 12
8 9 8 19 9 10 9 20
10 13 10 11 11 21 11 12
12 22 13 15 13 14
0 !NTHETA: angles
0 !NPHI: dihedrals
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0
1 0 !NGRP
0 0 0