[gmx-users] element symbol column in a pdb using editconf
Rebeca García Fandiño
regafan at hotmail.com
Tue Jul 7 16:42:04 CEST 2015
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 :-)
> 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
> Maybe, but first we need to know what command "doesn't work" or we don't
> know where the problem is :-)
> On Tue, Jul 7, 2015 at 4:15 PM Rebeca García Fandiño <regafan at hotmail.com>
> > 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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