[gmx-users] visualizing more than 9999 residues....

Anna Marabotti anna.marabotti at isa.cnr.it
Mon Feb 14 16:29:12 CET 2011

Dear gmx-users,
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).
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.
Thank you very much and sorry for this off-topic question.
Anna Marabotti
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
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