Hi Absalom,<br>
<br>
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.<br>
<br>
Hope this helps,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 3/24/06, <b class="gmail_sendername">Absalom Zamorano</b> <<a href="mailto:absalomz2002@yahoo.com.mx">absalomz2002@yahoo.com.mx</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi users gromacs, I want to simulate a interacction<br>between three peptides in a one box. So, once I have<br>the three gro files, I construct with genbox a box<br>from the largest peptide (this is OK), but when I want
<br>to introduce the second peptide ( genbox -cp<br>p1_largest_in_box.gro -ci peptide2.gro -nmol 1 -try<br>100 -o peptide_1_2_in_box.gro)<br>... the output is like:<br>/////////////<br>Program genbox, VERSION 3.3<br>Source code file: gmx_genbox.c, line: 307
<br>Fatal error:<br>more then one residue in insert molecules<br>program terminated<br>/////////////<br>What could I do to obtain this system with three<br>different peptides in box? This is because I want to<br>assambly them.
<br>I will really, really appreciate very much your commentaries..<br><br>Dr. Absalom Zamorano Carrillo<br>Profesor Titular A<br>Programa Institucional de Biomedicina Molecular, ENMyH-IPN<br>Guillermo Massieu Helguera #239 Fracc. "La Escalera"
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>