[gmx-users] problems with editconf 4.0

Berk Hess gmx3 at hotmail.com
Thu Nov 20 21:43:58 CET 2008


I assume this is 4.0 and not 4.0.2, right?
I fixed the problem of not having a box in editconf in 4.0.2.


Date: Thu, 20 Nov 2008 16:22:44 +0000
From: alanwilter at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] problems with editconf 4.0

So this command used to work fine:
editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0
Now, with gmx 4.0 (from fink for Mac Intel Leopard), I got a warning:
WARNING: No boxtype specified - distance condition applied in each dimension.
(no box information is inserted in the pdb file as it used to do in gmx 3)

and then when I try:
genbox -cp Complex.pdb -cs ffamber_tip3p.gro -o Complex_b4ion.pdb -p Complex.top
I get this error:
-------------------------------------------------------Program genbox, VERSION 4.0Source code file: gmx_genbox.c, line: 744

Fatal error:Undefined solute box.Create one with editconf or give explicit -box command line option-------------------------------------------------------
If I change '-o Complex.pdb' to '-o Complex.gro' and so on (i.e, if I use gro instead of pdb), all work fine.

So, pdb format is not ok anymore with gmx commands or there's a bug here?
Many thanks in advance,Alan-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate

Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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