Creating a polymer chain by importing a monomer structure from a PDB

alukard · March 31, 2025, 7:00pm

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 CRYST1 10.334 10.334 ATOM 1 H1 mol A 1 ATOM 2 C2 mol A 1 ATOM 3 C3 mol A 1 ATOM 4 O4 mol A 1 ATOM 5 C5 mol A 1 ATOM 6 O6 mol A 1 ATOM 7 C7 mol A 1 ATOM 8 C8 mol A 1 ATOM 9 C9 mol A 1 ATOM 10 C10 mol A 1 ATOM 11 C11 mol A 1 ATOM 12 C12 mol A 1 ATOM 13 C13 mol A 1 ATOM 14 O14 mol A 1 ATOM 15 O15 mol A 1 ATOM 16 H16 mol A 1 ATOM 17 H17 mol A 1 ATOM 18 H18 mol A 1 ATOM 19 H19 mol A 1 ATOM 20 H20 mol A 1 ATOM 21 H21 mol A 1 ATOM 22 H22 mol A 1 ATOM 23 H23 mol A 1 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 END
File test.psf
PSF BY OPEN BABEL 2.3.90
10.334 90.00 90.00 90.00 P 1 1
-0.016 -0.206 -5.819 1.00 0.00 mol H
-0.665 -2.130 3.842 1.00 0.00 mol C
-0.259 -0.689 3.518 1.00 0.00 mol C
-0.207 -0.528 2.111 1.00 0.00 mol O
0.169 0.658 1.594 1.00 0.00 mol C
0.471 1.634 2.284 1.00 0.00 mol O
0.188 0.664 0.102 1.00 0.00 mol C
-0.193 -0.469 -0.656 1.00 0.00 mol C
-0.160 -0.433 -2.064 1.00 0.00 mol C
0.255 0.735 -2.744 1.00 0.00 mol C
0.633 1.866 -1.988 1.00 0.00 mol C
0.599 1.831 -0.579 1.00 0.00 mol C
0.299 0.788 -4.246 1.00 0.00 mol C
0.657 1.787 -4.864 1.00 0.00 mol O
-0.086 -0.354 -4.873 1.00 0.00 mol O
-1.647 -2.362 3.431 1.00 0.00 mol H
0.716 -0.466 3.953 1.00 0.00 mol H
-0.978 0.011 3.945 1.00 0.00 mol H
-0.515 -1.378 -0.167 1.00 0.00 mol H
-0.456 -1.313 -2.617 1.00 0.00 mol H
0.954 2.770 -2.488 1.00 0.00 mol H
0.895 2.709 -0.022 1.00 0.00 mol H
0.050 -2.841 3.427 1.00 0.00 mol H
0 0 0 0 0 0 23 0 23 0

   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

veld · April 12, 2025, 9:20am

Dear user,

Unfortunately, the above test.pdb does not abide by PDB standards, since PDB is a fixed format standard. Consequently, I cannot import it. Could you provide the correct fixed format file?

Could you also tell us, what kind of monomer this is? It looks like, that this monomer’s repeat unit is represented by SMILES *COC(=O)c1ccc(cc1)C(=O)OC*, but in your structure one oxygen has a spurious hydrogen connected to it.

Are you intending to create an amorphous melt or a crystalline surface?

Thanks!

alukard · April 12, 2025, 3:30pm

Hello, I am attaching my test.pdb file. I want to create a polymer chain of amorphous polyethylene terephthalate, so ethylene terephthalate itself is represented as the monomer. I use hydrogen atoms to close the end groups of the polymer chain.

test.pdb (3.7 KB)