[gmx-users] editconf/genbox problem in Gromacs 4.0
gmx3 at hotmail.com
Fri Nov 7 12:19:02 CET 2008
For the moment you can use editconf of 3.3
or copy a cryst1 entry (one of the first lines) from another pdb file
into you pdb input file, editconf will then write the correct box in the output pdb.
> Date: Fri, 7 Nov 2008 12:13:55 +0100
> From: caterina.arcangeli at casaccia.enea.it
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0
> Many thanks to Bert and Xavier.
> >> Dear gmx-users,
> >> I have encountered a similar editconf/genbox problem posted by Matt
> >> Danielson on 14 October:
> >> I 'm using Gromacs 4.0 (installed on MacOS).
> >> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o
> >> may_protein_box.pdb
> > use gro files for output and it works. The box size is not written
> > in the pdb file, although it used to be.
> Yes, it works, but I'm using .pdb instead of .gro format to support
> chain identifiers since my system is composed by 3 protein chains.
> So I will wait for the new 4.0.1 release.
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