[gmx-users] Question about generating top file with different angle functions (Mark Abraham)

[Zhenhai Li]

Hi Mark,

Thanks for your reply. I think I didn't phrase my question clear. Actually
what I am trying to do is generating top file with pdb2gmx command. Since
for each force field, there's a default bond function type, angle function
type, dihedral function type. If I am using a force field, in which part of
the residue using function 1, part of residue using function 2, is it
possible to modify .rtp file, and generate correct top file simply with
command pdb2gmx. For example, if the default angle function type is 1, but
it is 5 in residue A, when I generate .top file, all the angle in residue A
will be assigned with type 1 instead of 5.

And I tried adding what you suggested in .rtp file, and generate the .top
file. It shows up like this:
   68    67    72     1        5    1100.0 120.0
    i       j       k     type   type   parameters

Which means the function type are assigned twice. So I guess you are
suggesting adding the parameters in ffbonded.itp. But actually I have that
in ffbonded.itp. However because the assigned angle type is incorrect in
.top file,  grompp cannot work properly. However with your suggestion, I
think I can simplify the script by adding a mark on the angle, which is in
need of modification.

The following is what you suggested:
[angles]
N C O 5 1000.0 120.0 ;


Thank you very much.

Zhenhai


> Date: Thu, 06 Aug 2015 07:12:50 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Question about generating top file with
>         different angle functions
> Message-ID:
>         <CAMNuMASan_+5N6GQgaYstUZebsyeEE8T8Zy-da=VfCBD+N=
> CRg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Thu, Aug 6, 2015 at 9:02 AM Zhenhai Li <shibalagu.thu at gmail.com> wrote:
>
> > Hi Aishwary,
> >
> > 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.
> >
>
> I would have expected
>
> [angles]
> N C O 5 1000.0 120.0 ; ie whatever the actual parameters are
>
> would over-ride the default (ie. angletype of 3 and let grompp look up the
> parameters) but I'm not sure that that's what your original post claims.
>
> Mark
>
>
> > Thanks a lot.
> >
> > Zhenhai
> >
> >
> > > 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.
> > > Message-ID:
> > >         <CAJ=
> > > 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>
> > > wrote:
> > >
> > > > Dear GMX-users,
> > > >
> > > > Recently I am trying to adding a residue to a force field. I have
> > > followed
> > > > the instruction of "how to adding residue" on the website. And right
> > now
> > > I
> > > > can generate the top file from PDB file with pdb2gmx command. However
> > > some
> > > > 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
> > > angle
> > > > function of the new residue in the top file generated by pdb2gmx. And
> > > when
> > > > 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
> > > type?
> > > >
> > > > Thank you very much
> > > >
> > > > --
> > > > Zhenhai
> > > > --
> > > > Gromacs Users mailing list
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> > >
> > >
> >
> > --
> > Zhenhai
> > --
>

-- 
Zhenhai