[gmx-users] element symbol column in a pdb using editconf
Rebeca García Fandiño
regafan at hotmail.com
Tue Jul 7 18:10:00 CEST 2015
Done!
http://redmine.gromacs.org/issues/1307
> From: mark.j.abraham at gmail.com
> Date: Tue, 7 Jul 2015 15:48:56 +0000
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] element symbol column in a pdb using editconf
>
> Hi,
>
> That surprises me. Can you please upload your inputs to
> http://redmine.gromacs.org/issues/1307 and I can take a look?
>
> Mark
>
> On Tue, Jul 7, 2015 at 5:19 PM Rebeca García Fandiño <regafan at hotmail.com>
> wrote:
>
> > Hi Mark,
> > I just tried both proposals:
> >
> > 1) gmx editconf -f input.tpr -o output.pdb
> >
> > Where output.pdb is:
> >
> > (...)
> > ATOM 1 C MOL 1 28.780 30.430 14.380 1.00 0.00
> > ATOM 2 C0 MOL 1 32.260 29.290 13.120 1.00 0.00
> > ATOM 3 C1 MOL 1 27.970 30.090 15.640 1.00 0.00
> > (...)
> >
> > 2) gmx trjconv -s topol.tpr -f input.gro -o output2.pdb
> >
> > where output2.pdb is:
> >
> > (...)
> > ATOM 1 C MOL 1 28.770 30.460 14.390 1.00 0.00
> > ATOM 2 C0 MOL 1 32.270 29.290 13.110 1.00 0.00
> > ATOM 3 C1 MOL 1 27.960 30.090 15.640 1.00 0.00
> > (...)
> >
> > So, it seems that at the moment, there is no way to introduce this column
> > in GROMACS, is it correct?
> >
> > Cheers,
> >
> > Rebeca.
> >
> > > From: mark.j.abraham at gmail.com
> > > Date: Tue, 7 Jul 2015 15:02:48 +0000
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] element symbol column in a pdb using editconf
> > >
> > > Hi,
> > >
> > > OK - you're not using a .tpr file, which that redmine issue hints will be
> > > needed in order to get the elements identified (because machinery to
> > guess
> > > element symbols from atom names in .gro is nobody's idea of a good time).
> > >
> > > I expect gmx editconf -f input.tpr -o output.pdb would work for you, but
> > > might not be convenient. I suspect gmx trjconv -s topol.tpr -f input.gro
> > -o
> > > output.pdb might use the fixed machinery and do what you want.
> > >
> > > Mark
> > >
> > > On Tue, Jul 7, 2015 at 4:42 PM Rebeca García Fandiño <
> > regafan at hotmail.com>
> > > wrote:
> > >
> > > > Sorry, I did not mention because it was a simple editconf:
> > > >
> > > > editconf -f file.gro -o file.pdb
> > > >
> > > > What I am trying to obtain was a file.pdb with the element symbol
> > column
> > > > included.
> > > >
> > > > In other words, what I am obtaining is something like:
> > > >
> > > > ATOM 1 C MOL 1 -1.140 0.440 0.000 1.00 0.00
> > > > ATOM 2 C0 MOL 1 2.330 -0.730 -1.260 1.00 0.00
> > > > ATOM 3 C1 MOL 1 -1.950 0.060 1.260 1.00 0.00
> > > > (...)
> > > >
> > > > and I would like to obtain a file.pdb like this
> > > >
> > > > ATOM 1 C MOL 1 -1.135 0.409 0.000 1.00 0.00
> > > > C
> > > > ATOM 2 C0 MOL 1 2.336 -0.737 -1.258 1.00 0.00
> > > > C
> > > > ATOM 3 C1 MOL 1 -1.953 0.061 1.257 1.00 0.00
> > > > C
> > > > (...)
> > > >
> > > > I hope it is clearer now :-)
> > > >
> > > > Cheers,
> > > >
> > > > Rebeca.
> > > >
> > > >
> > > >
> > > > > From: mark.j.abraham at gmail.com
> > > > > Date: Tue, 7 Jul 2015 14:31:22 +0000
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: Re: [gmx-users] element symbol column in a pdb using
> > editconf
> > > > >
> > > > > Hi,
> > > > >
> > > > > Maybe, but first we need to know what command "doesn't work" or we
> > don't
> > > > > know where the problem is :-)
> > > > >
> > > > > Mark
> > > > >
> > > > > On Tue, Jul 7, 2015 at 4:15 PM Rebeca García Fandiño <
> > > > regafan at hotmail.com>
> > > > > wrote:
> > > > >
> > > > > > Dear Gromacs users,
> > > > > > I am trying to obtain a pdb file, using editconf, with the element
> > > > symbol
> > > > > > column.
> > > > > >
> > > > > > Looking for that, I found this revision:
> > > > > >
> > > > > > http://redmine.gromacs.org/issues/1307
> > > > > >
> > > > > > It
> > > > > > seems to be resolved, however, I am using GROMACS 5.0.4 and it is
> > not
> > > > > > working. Is there any way to retain the element symbol column in
> > the
> > > > > > pdb using editconf?
> > > > > >
> > > > > > Thanks a lot in advance,
> > > > > >
> > > > > > Best wishes,
> > > > > >
> > > > > > Dr. Rebeca Garcia
> > > > > > Santiago de Compostela University
> > > > > > Spain
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
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