[gmx-users] About .rtp File

[João Martins]

Unless specified in your mdp that you're using position restraints, by
default it won't use them.

The command is:

define = -DPOSRES


and you should see:

; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
> #endif


either after the molecule topology inside the .top file or at the end of a
separate topology file loaded by the top file, depending on which version
you're using. By the way, that's automatic, nothing wrong with the .rtp,
pdb2gmx just creates a position restraint file for heavy atoms
automatically by default. When in doubt, check the manuals.




*Joao Martins*

joaomartins139 at gmail.com

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.  The oplsaa.ff directory
> for whatever reason doesn't have the residuetypes.dat (Gromacs v. 5.0.1)
> but I got everything to work.
>
> 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.
>
> 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
> >>  --
> >>  Gromacs Users mailing list
> >>
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> --
> Mohd Farid Ismail
> mohd.farid.ismail at yandex.com
> --
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