[gmx-users] About .rtp File

[Mark Abraham]

On Tue, Sep 16, 2014 at 10:09 AM, Mohd Farid Ismail <
mohd.farid.ismail at yandex.com> wrote:

> Thank you Joao Martins.  I figured it out eventually, but it would've been
> easier if the manual is more explicit about this.


True, but there's
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
in the meantime.


> The oplsaa.ff directory for whatever reason doesn't have the
> residuetypes.dat (Gromacs v. 5.0.1) but I got everything to work.
>

Joao got that detail wrong. residuetypes.dat is shared by all force fields,
so lives in the directory above it (and said directory can be your working
directory, so you don't have to modify the system installation)


> One other question I have, is that pdb2gmx created a .top topology file
> and .itp file that apparently contains the constraints for heavy atoms.  I
> don't intend to have these constraints, and I haven't comb the manual or
> search the mailing list yet.  Is there anything in the .rtp file that I
> miss?  Can I delete these constraints?  The system is just a test system of
> 4000 1-propanol, using opls-aa.  Any input is appreciated.
>

Position restraints are not on by default - but you should get your
terminology straight - see
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

Mark


> Best regards,
> --Farid
>
> 16.09.2014, 14:24, "João Martins" <joaomartins139 at gmail.com>:
> > You need to create the R21.rtp and place it in the same folder as your
> > forcefield. You also need to edit your residuetypes.dat inside your
> > forcefield for pdb2gmx to know what to do with that type of molecule.
> Other
> > than that, and if I didn't forget anything, you just need to add any new
> > atomtypes, bond, angles or dihedrals you created for your molecule.
> >
> > *Joao Martins*
> >
> > joaomartins139 at gmail.com
> >
> > On Tue, Sep 16, 2014 at 5:45 AM, Mohd Farid Ismail <
> > mohd.farid.ismail at yandex.com> wrote:
> >>  Hi, how would one use the .rtp file with pdb2gmx?  Is pdb2gmx supposed
> to
> >>  just find the .rtp file in the local directory?
> >>
> >>  I wanted to create an entry for a new residue using oplsaa.  However,
> >>  (assuming I build the .rtp file correctly), the pdb2gmx file wouldn't
> >>  recognized the residue 'R21' with the error "Residue 'R21' not found in
> >>  residue topology file.  The file R21.rtp is in the local directory.
> >>
> >>  --
> >>  Mohd Farid Ismail
> >>  mohd.farid.ismail at yandex.com
> >>  --
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> --
> Mohd Farid Ismail
> mohd.farid.ismail at yandex.com
> --
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