[gmx-users] element symbol column in a pdb using editconf

[Rebeca García Fandiño]

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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