[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

[Elton Carvalho]

Hello, fellow Gromacs Users,

I'm trying to model P3DDT with CGenFF according to the instructions at
paramchem.org, running the cgenff_charmm2gmx.py script as provided in
their website. All this is being done on gromacs 2016.

The script converts the .str file generated by paramchem.org to
gromacs syntax and units. As a first test, I ran a signle
dodecylthiophene molecule through the process and obtained apparently
sane .top and .itp files. The .itp file #includes a .prm file, that
contains the parameters fitted by the paramchem software.

When running gmx grompp (version 2016), I get these two warnings:

=== GROMPP WARNING BEGIN ===

WARNING 1 [file ddt.prm, line 17]:
  Overriding Proper Dih. parameters.
  Use dihedraltype 9 to allow several multiplicity terms. Only consecutive
  lines are combined. Non-consective lines overwrite each other.

  old:                                          0 0.8368 1 0 0.8368 1
  new: CG2R51   CG2R51    CG321    CG321     9     0.000000     1.129680     2


WARNING 2 [file ddt.prm, line 18]:
  Overriding Proper Dih. parameters.
  Use dihedraltype 9 to allow several multiplicity terms. Only consecutive
  lines are combined. Non-consective lines overwrite each other.

  old:                                          0 1.12968 2 0 1.12968 2
  new: CG2R51   CG2R51    CG321    CG321     9     0.000000     0.000000     3

=== GROMPP WARNING END ===

But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
and 18 of the reffered file, as follows:

=== ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===

[ dihedraltypes ]
;      i        j        k        l  func         phi0         kphi  mult
  CG2R51   CG2R51   CG2R51    CG321     9   180.000000    16.736000     2
   CG321   CG2R51   CG2R51   SG2R50     9   180.000000    29.288000     2
   CG321   CG2R51   CG2R51    HGR51     9   180.000000     4.184000     2
  CG2R51   CG2R51    CG321    CG321     9     0.000000     0.836800     1
  CG2R51   CG2R51    CG321    CG321     9     0.000000     1.129680     2
  CG2R51   CG2R51    CG321    CG321     9     0.000000     0.000000     3
  CG2R51    CG321    CG321    CG321     9     0.000000     0.167360     3
  CG2R51    CG321    CG321     HGA2     9     0.000000     0.836800     3

=== ddt.prm RELEVANT SECTION END ===

As you can see, the dihedraltype is 9 and the different multiplicities
of the "CG2R51   CG2R51    CG321    CG321" dihedral are on adjacent
lines (16, 17 and 18 of the original file. Note that the first warning
is about overriding the parameters on line 16 with those on line 17,
so this dihedral is not defined somewhere else).  No wildcard dihedral
parameters are present in the loaded .itp files.

Why does grompp warn me that it's "Overriding Proper Dih. parameters",
even though the parameters are entered (to the best of my knowledge)
as instructed both in the warning and in Section 5.3.3 of the
Reference Manual? How can I check whether it really did override the
parameter or added the different terms?

Thanks in advance,
-- 
Elton Carvalho