[gmx-users] Dihedral calculations in topology

[Kamps, M.]

Dear Mark,

Thanks for your reply!
I am replicating Polyethylene, of which the [polymer.rtp] and the
[polymer.hdb] are exactly the same as described by Justin Lemkul in
this link: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html

So, my rtp entries are:
; Terminal PE residue (chain "begin")
;    C1 is -CH3
[ EthB ]
 [ atoms ]
    C1    opls_135   -0.180     1
   H11    opls_140    0.060     1
   H12    opls_140    0.060     1
   H13    opls_140    0.060    1
    C2    opls_136   -0.120     2
   H21    opls_140    0.060     2
   H22    opls_140    0.060     2
 [ bonds ]
    C1   H11
    C1   H12
    C1   H13
    C1   C2
    C2   H21
    C2   H22
    C2   +C1
; Terminal PE residue (chain "end")
;    C2 is -CH3
[ EthE ]
 [ atoms ]
    C1    opls_136   -0.120     1
   H11    opls_140    0.060     1
   H12    opls_140    0.060     1
    C2    opls_135   -0.180     2
   H21    opls_140    0.060     2
   H22    opls_140    0.060     2
   H23    opls_140    0.060    2
 [ bonds ]
    C1   -C2
    C1   H11
    C1   H12
    C1   C2
    C2   H21
    C2   H22
    C2   H23

And the used hdb entries are:
EthB  2
3     4     H1     C1     C2     +C1
2     6     H2     C2     C1     +C1
EthE  2
2     6     H1     C1     C2     -C2
3     4     H2     C2     C1     -C2

The used pdb file is:
ATOM      1  C1  EthB    1       0.000   0.000   0.000
ATOM      2  C2  EthB    1       1.273   0.847   0.000
ATOM      3  C1  EthE    1       2.546   0.000   0.000
ATOM      4  C2  EthE    1       3.818   0.847   0.000

Which is a simple C4H10 molecule, composed out of two residues, with a
total of three dihedrals. The output given by grompp is:
Setting the LD random seed to -962199660
Generated 337431 of the 337431 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 337431 of the 337431 1-4 parameter combinations
ERROR 1 [file topol_polymer.itp, line 119]:
  No default Proper Dih. types
ERROR 2 [file topol_polymer.itp, line 120]:
  No default Proper Dih. types
ERROR 3 [file topol_polymer.itp, line 121]:
  No default Proper Dih. types
Where lines 119 till 121 correspond with the three dihedrals in my
topology (of the polymer).

The output of pdb2gmx is as follows:
Opening force field file ./oplsaa_polymer.ff/aminoacids.r2b
Reading C4H10.pdb...
Read 4 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 2 residues with 4 atoms

  chain  #res #atoms
  1 ' '     2      4

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./oplsaa_polymer.ff/atomtypes.atp
Atomtype 823
Reading residue database... (oplsaa_polymer)
Opening force field file ./oplsaa_polymer.ff/Polymer.rtp
Reading .rtp file without '[ bondedtypes ]' directive,
Will proceed as if the entry was:
[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions
HH14  remove_dih
     1       1          1          2               0               3
           1              1

Residue 4
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/aminoacids.rtp
Residue 55
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/surface.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a
proper dihedral
Residue 62Warning: file does not end with a newline, last line:
    PT    PT   0.000     0
Residue 63
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/Polymer.hdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.hdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.n.tdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.c.tdb
Processing chain 1 (4 atoms, 2 residues)
Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 2 residues with 14 atoms
Making bonds...
Number of bonds was 14, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Making cmap torsions...
There are    3 dihedrals,    0 impropers,   24 angles
            27 pairs,       13 bonds and     0 virtual sites
Total mass 58.124 a.m.u.
Total charge -0.000 e
Writing topology
Writing coordinate file...