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<DIV><FONT size=2 face=Arial><SPAN class=905360915-14022011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=905360915-14022011>I have a system
formed by protein+ligand+lipid bilayer that accounts for about 10500 residues
(56000 atoms). It seems to me that it is not possible to visualize correctly
such a large system with Pymol or VMD, because it seems that the max number of
residues that I can manage with both programs is exactly 9999. Moreover, it's
not only a visualization problem, since I also had several problems trying
to use Pymol or VMD to create the system in which the protein+ligand is
correctly oriented with respect to the lipid bilayer, to proceed further with
g_membed. I had several problems in saving the .pdb file (after the 9999th
residue, the numbering restarted from 0; when I manually corrected this prroblem
and re-numbered the file, I opened it with VMD and Python and found some
aberrant visualization of the water molecules exceeding the number of 9999. At
last, I decided to remove the exceeding waters).</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=905360915-14022011>I know that this is
a Gromacs user list, not a Pymol or VMD user list, but since it seems to me that
these two programs are generally considered as a "graphical interface" with
respect to Gromacs, I'd like to know how you folks manage this problem without
removing residues. I searched for some hints in the gmx-user list and in Google
but I didn't find anything.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=905360915-14022011>Thank you very much
and sorry for this off-topic question.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=905360915-14022011>Anna
Marabotti</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV align=left>
<DIV dir=ltr align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science -
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV></DIV>
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