[gmx-users] editconf/genbox problem in Gromacs 4.0
caterina.arcangeli at casaccia.enea.it
Fri Nov 7 12:22:29 CET 2008
Thanks again Berk.
2008/11/7 Berk Hess <gmx3 at hotmail.com>:
> 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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