[gmx-users] Dihedral calculations in topology

Kamps, M. m.kamps at student.rug.nl
Wed Dec 21 11:16:52 CET 2016

Dear GMX users,

I have a few questions about something I don’t fully understand. I am
trying to work with polymers, where the basics are written by Justin
Lemkul via this link:

This works up to the point where I want to use grompp, where it gives
errors regarding the Proper Dihedral types; No default Proper Dih.
types. When consulting the lines where these errors refers to, it is
caused by the three dihedrals defined in my topology:

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    2     1     5     8     1
    1     5     8    11     1
    5     8    11    12     1

Now, according to the manual table 5.5, page 138 (v. 2016.1), these
three dihedrals are defined as funct=1, which corresponds with a
proper dihedral, while by default the OPLS ff only knows R-B
dihedrals, which are funct=3. Up to this point my story is correct

Then, why does pdb2gmx select this dihedral type? In the above
topology [ai aj ak al] = [1 5 8 11] refers to a [opls_135 opls_136
opls_136 opls_135] dihedral, which I believe is a [CT CT CT CT]
dihedral. This dihedral is already defined by ffbonded.itp as follows:
  CT     CT     CT     CT      3      2.92880  -1.46440   0.20920
-1.67360   0.00000   0.00000 ; hydrocarbon all-atom
Am I correct about this part?

Is it valid to manually change the funct=1 in the above topology to
funct=3 to use this dihedral type? And if it is valid, how can I
prevent pdb2gmx to assign a funct=1 to the topology?


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