[gmx-users] Dihedral calculations in topology

[Mark Abraham]

Hi,

On Wed, Dec 21, 2016 at 9:17 PM Kamps, M. <m.kamps at student.rug.nl> wrote:

> 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:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
>
> 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
> right?
>

The normal [bondedtypes] defaults in oplsaa.ff/aminoacids.rtp uses dihedral
type 3, yes. Whether that's applicable to your case we can't tell. Which
file are your .rtp entries coming from? The terminal output of pdb2gmx and
grompp say a lot of useful things about which it would be nice not to guess.

Mark

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?
>
> Mark
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