Several users have reported this problem, i.e.:
http://www.gromacs.org/pipermail/gmx-users/2008-November/038181.html
Perhaps try upgrading to version 4.0.2 and try again.
-Justin
Bernhard Knapp wrote:
Dear users
I am trying to minimize the energy of a complex using gromacs 4. The
commands are the following:
pdb2gmx -f full_mCARKL_to_xylose_kinaseFH.pdb -o
full_mCARKL_to_xylose_kinaseFH.gro.pdb -p
full_mCARKL_to_xylose_kinaseFH.top -ignh
editconf -f full_mCARKL_to_xylose_kinaseFH.gro.pdb -o
full_mCARKL_to_xylose_kinaseFH.cube.pdb -bt cubic -d 2.0
genbox -cp full_mCARKL_to_xylose_kinaseFH.cube.pdb -cs spc216.gro -o
full_mCARKL_to_xylose_kinaseFH.water.pdb -p
full_mCARKL_to_xylose_kinaseFH.top -nice 0
after genbox it stops with the 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
-------------------------------------------------------
Although this is definitly not true since the box has been created with
editconf (and not error is given by it). If I try the same commands (and
complex) on Gromacs 3.3 it works fine without error. Any ideas?
Thank you in advance
Bernhard
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
