[gmx-users] Dihedral calculations in topology

[Mark Abraham]

Hi,

pdb2gmx told you that it saw that your rtp file didn't have default
bondedtypes, so it was going to use certain values, and that means default
dihedral type 1. If you want to use the same defaults as aminoacids.rtp,
then copy them over to the rtp file you're using :-)

Mark

On Wed, Dec 21, 2016 at 10:12 PM Kamps, M. <m.kamps at student.rug.nl> wrote:

> 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...
> --
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