[gmx-users] Question about generating top file with different angle functions
shibalagu.thu at gmail.com
Thu Aug 6 09:01:38 CEST 2015
Thank you very much for your reply. So I guess the answer to my question is
there's no way to overwrite the angle function type for specific angle
interaction by changing .rtp file or other like ffbond.itp files in force
field. Then I will save my time from investigating how to change .rtp file
or other files in force field folder, and focus on writing a script.
Thanks a lot.
> Date: Thu, 6 Aug 2015 09:44:26 +0530
> From: Aishwary Shivgan <aishwaryshivgan55 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Question about generating top file with
> different angle functions.
> XXZV8W+aEWzXOZYDUGYADzf9szocBSfJ81Jnv9ufvqd1Mvw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> Once you define the [ bondedtypes ] in the rtp file like this.
> 1 1 3 1 1 3 1 0
> here the dihedral type function is 3 that means all the dihedrals you
> define in the aminoacids.rtp file will be taken as type 3. Even I had the
> the same problem, I was using function type 3 and 5, pdb2gmx takes
> function 5 as 3. Not a problem you can write a script or do it manually to
> replace the number 5 to 3.
> On Thu, Aug 6, 2015 at 8:26 AM, Zhenhai Li <shibalagu.thu at gmail.com>
> > Dear GMX-users,
> > Recently I am trying to adding a residue to a force field. I have
> > the instruction of "how to adding residue" on the website. And right now
> > can generate the top file from PDB file with pdb2gmx command. However
> > of the angle function in the residue is different from the default one in
> > rtp file in the force field. Therefore there are some mistake on the
> > function of the new residue in the top file generated by pdb2gmx. And
> > I use grompp command to generate .tpr file, I will get error like "No
> > default U-B types"
> > I am not sure if there's a way to define angle type for specific angle
> > interaction in force field to make pdb2gmx overwrite angle function type
> > for those angle interaction, or I have to manually change those angle
> > Thank you very much
> > --
> > Zhenhai
> > --
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