[gmx-users] problems with editconf 4.0

Alan alanwilter at gmail.com
Thu Nov 20 17:22:44 CET 2008

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

(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 4.0
Source 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 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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