[gmx-users] About .rtp File

[Mohd Farid Ismail]

Thank you Dr. Martins. Eu aprecio sua ajuda.

--Farid

16.09.2014, 16:40, "João Martins" <joaomartins139 at gmail.com>:
> 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
>>>>   --
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>>  --
>>  Mohd Farid Ismail
>>  mohd.farid.ismail at yandex.com
>>  --
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--
Mohd Farid Ismail
mohd.farid.ismail at yandex.com