[gmx-users] genion: -pot fails to produce .pdb file

Stud_Psychopharm stu_psyc at nimhans.kar.nic.in
Mon Feb 2 18:34:01 CET 2004

you can try with this way.. instead of -pot just give 
-o outputfilename.pdb 
>genion -s input.tpr -nn 2 -o output.pdb -rmin 2 (in the case of two or 
more Cl)
all the best
"The more we learn the more we realize how little we know." - 
R.Buckminster Fuller 

Blaise M.Costa
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.

-----Original Message-----
From: "Madhuri Agashe" <magashe at CLEMSON.EDU>
To: <gmx-users at gromacs.org>
Date: Sun, 1 Feb 2004 21:30:33 -0500
Subject: [gmx-users] genion: -pot fails to produce .pdb file

> I am using the genion command to replace few solvent atoms by Na and Cl
> ions.
> I want this command to also generate a .pdb output file in addition to
> the
> ..gro file. Hence I specified the -pot option, but no .pdb file was
> created.
> I have used this command before and it has worked successfully.
> There have been no changes in parameters. The system comprises of a
> self
> assembled monolayer surface of methyl and a protein segment at a
> distance of
> 5Au from the surface.
> Why should this happen??
> -Madhuri
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