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

[Mark Abraham]

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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