[gmx-users] About to introduce more than one protein in a box....

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 24 23:08:20 CET 2006

Hi Absalom,

You could position your peptides using editconf and write three pdb files.
Then if you grep all "ATOM" records to a new pdb file, everything will be as
one! Construct a box, solvate, et voila! Alternatively, you can load all
three peptides into Pymol (as pdb files), move and reposition them using the
mouse, just the way you want to have them, write a pdb file of all three
together, construct a box, solvate, et voila! You may have to force Pymol to
keep the original order of the atoms, otherwise the resulting pdb file might
not correspond to the topology file.

Hope this helps,


On 3/24/06, Absalom Zamorano <absalomz2002 at yahoo.com.mx> wrote:
> Hi users gromacs, I want to simulate a interacction
> between three peptides  in a one box. So, once I have
> the three gro files,  I construct with genbox a box
> from the largest peptide (this is OK), but when I want
> to introduce the second peptide ( genbox -cp
> p1_largest_in_box.gro -ci peptide2.gro -nmol 1 -try
> 100 -o peptide_1_2_in_box.gro)
> ... the output is like:
> /////////////
> Program genbox, VERSION 3.3
> Source code file: gmx_genbox.c, line: 307
> Fatal error:
> more then one residue in insert molecules
> program terminated
> /////////////
> What could I do to obtain this system with three
> different peptides in box? This is because  I want to
> assambly them.
> I will really, really appreciate very much your commentaries..
> Dr. Absalom Zamorano Carrillo
> Profesor Titular A
> Programa Institucional de Biomedicina Molecular, ENMyH-IPN
> Guillermo Massieu  Helguera  #239 Fracc. "La Escalera"
> Ticomán, D.F. México, C.P  07320
> Tel. (55) 57296000,  ext 55542
> ___________________________________________________________
> Do You Yahoo!?
> La mejor conexión a Internet y <b >2GB</b> extra a tu correo por $100 al
> mes. http://net.yahoo.com.mx
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060324/39a17545/attachment.html>

More information about the gromacs.org_gmx-users mailing list