[gmx-users] Overriding Wildcard dihedraltypes

Mark Abraham mark.j.abraham at gmail.com
Thu Jan 9 16:49:07 CET 2014


Thanks for the question, and particularly the detail. It seems that you are
trying use a [dihedraltypes] section in my_molecule.itp, which is generally
a bad idea, because all such directives must appear before the first
[molecule] directive, which defeats the point of molecule.itp files being
somewhat movable. Because of that intention for molecule.itp files, there'd
be no reason to have separate [dihedraltypes] sections that should be
logically treated together, so the code assumes such sections are
separable, and so you get unintended behaviour (perhaps particularly with
wildcard atom types, and/or type 9 dihedrals) unless you change
ffbonded.itp like you have now done.

Recommended procedures are
* to copy the charmm36.ff directory into your working directory and modify
ffbonded.itp to work like you want it to, or
* to give explicit parameters in the [dihedrals] section of your
molecule.itp (*not* [dihedraltypes]), so that the parameter lookup from
[dihedraltypes] is not invoked at all. Note that the behaviour for multiple
matching [dihedrals] is to add the functions; the behaviour for multiple
matching [dihedraltypes] is to override earlier functions (except for type


On Thu, Jan 9, 2014 at 2:30 PM, hubert santuz <hubert.santuz at gmail.com>wrote:

> Dear Gromacs Users,
> I'm trying to set up a molecule into the charmm36 force field for lipids.
> I correctly obtained a good itp file from a charmm file.
> In this itp file, a wildcard dihedraltype (from the ffbonded.itp) is
> overrided by an explicit dihedraltype :
> In ffbonded.itp :
> X    CTL1    CTL2    X    9    0.00    0.8368    3
> In my itp file:
> CRL1   CTL1   CTL2   CTL2     9    180.00       0.50961    3
> CRL1   CTL1   CTL2   CTL2     9    180.00       0.91002    2
> CRL1   CTL1   CTL2   CTL2     9    180.00       1.00332    1
> In my topol.top:
> #include "charmm36.ff/forcefield.itp"
> #include "my_molecule.itp"
> Unfortunately, this override is not taking in account by gromacs.
> When I dump the tpr, I do not see this 3 types in the "functype" lines.
> However, when I add this override into the ffbonded.itp file before the
> wildcard dihedraltype like this :
> In ffbonded.itp:
> CRL1   CTL1   CTL2   CTL2     9    180.00       0.50961    3
> CRL1   CTL1   CTL2   CTL2     9    180.00       0.91002    2
> CRL1   CTL1   CTL2   CTL2     9    180.00       1.00332    1
> X    CTL1    CTL2    X    9    0.00    0.8368    3
> In this case, I can see clearly the 3 dihedraltypes in my tpr.
> More interestingly, when I try to override an explicit dihedral type from
> ffbonded.itp (like CEL1 CTL2 CEL1 HEL1) into my itp file, I get a warning
> from grompp and I see the override in the tpr file.
> It seems that wildcard dihedral types cannot be override (at least with
> the function 9, I didn't test with other forcefields).
> For the moment, the only solution that I have found is either to :
>    - add the override in the ffbonded.itp which is not a good idea.
>    - or add 2 new atoms with new names but with the same parameters than
> (CTL1 and CTL2) in my itp file and change the dihedraltype according to
> these two new atoms.
> Without this override, I'm not able to reproduce the correct dihedral
> energy from a SPE calculation between gromacs and namd... (but with the
> override, I am!)
> Have people already experienced this case ?
> Also, I can provide test files (itp, top, pdb) with only 4 atoms and this
> dihedral.
> Thanks for the help!
> Best regards,
> Hubert
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list