[gmx-users] element symbol column in a pdb using editconf
Mark Abraham
mark.j.abraham at gmail.com
Tue Jul 7 17:49:08 CEST 2015
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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