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

[Tsjerk Wassenaar]

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,

Tsjerk

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
>
>
>
>
>
>
>
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--

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
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