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: [email protected] 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"
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
