[gmx-users] About .rtp File

[Mohd Farid Ismail]

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
>>  --
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--
Mohd Farid Ismail
mohd.farid.ismail at yandex.com