[gmx-users] pdb2gmx angles and dihedrals

Mark Abraham Mark.Abraham at anu.edu.au
Sat May 5 07:06:40 CEST 2012

On 5/05/2012 1:47 AM, Elton Carvalho wrote:
> Dear Gromacs users
> I am currently preparing an RTP file to describe a polymer for use with MARTINI.
> MARTINI does not include default bonded interactions, so all bonds,
> angles and dihedrals must be explicitly defined in the topology file
> or, in my case, in the RTP file.
> The problem is that pdb2gmx generates at least one dihedral for each
> bond and an angle for each pair of bonds sharing an atom, even it they
> are not explicitly defined in the RTP. In that case, pdb2gmx will
> include the triplet (or quadruplet) for the angle (or dihedral), but
> with empty parameters, so that grompp looks for general parameters in
> the forcefield ITP file.
> With coarse-graned forcefields, it does not necessarily make sense to
> have all angles and dihedrals, since, for example, rings are modelled
> as triangles of beads (so that the angles are redundant with the bond
> lengths) and trans alkyl chains are modelled as colinear beads (such
> that a dihedral is undefined).
> Is there a way to prevent pdb2gmx from creating these angles and
> dihedrals, unless explicity defined in the RTP?

Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have 
supposed Martini has some kind of builder program other than pdb2gmx, 
for this kind of reason, but I have no idea whether this is true.

Setting nrexcl = 1 would exclude such angles and dihedrals, I think, but 
would also exclude generating the normal ones. One option is to do that 
and explicitly define the relevant angles and dihedrals.

> Also, the manual states the following regarding RTP files:
> "The first field in the file is the [ bondedtypes ] field, which is
> followed by four numbers, indicating
> the interaction type for bonds, angles, dihedrals, and improper dihedrals. "
> And includes this as an example:
> [ bondedtypes ] ; mandatory
> ; bonds angles dihedrals impropers
> 1       1       1       2  ; mandatory
> But the aminoacids.rtp file included in the opls-aa forcefield starts with:
> [ bondedtypes ]
> ; Col 1: Type of bond
> ; Col 2: Type of angles
> ; Col 3: Type of proper dihedrals
> ; Col 4: Type of improper dihedrals
> ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
> ; Col 6: Number of excluded neighbors for nonbonded interactions
> ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
> ; Col 8: Remove propers over the same bond as an improper if it is 1
> ; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
>      1       1          3          1        1         3      1     0
> Which is inconsistent with the manual. In particular, Col8 set to 1
> seems to remove dihedrals over bonds with any dihedral, not only those
> defined under the  [ impropers ] directive.

Code comments are in disagreement about column 8. Looking at the code, I 
think the above .rtp comment is how the code works. A specific simple 
counter-example (showing how .rtp contents create .itp contents that 
seem to breach the above description) would be welcome. I'm not sure if 
there are circumstances where impropers are generated automatically, but 
that could possibly explain such an observation.

> Could anyone clarify the role of these extra columns? I think this
> also hints for a review in this section of the manual.

True. An update is in progress now.


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