What you suggested, worked. I mean not resname POPC solved the problem. But I'd like to know why that problem happens?! I followed the steps of KALP15 exactly.
Anyway, thanks Peter. Sincerely, Shima ----- Original Message ----- From: Peter C. Lai <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Sent: Saturday, September 22, 2012 9:57 AM Subject: Re: [gmx-users] Visualizing the system This is a VMD question, but try using manual selections, like: "not resname POPC and not resname SOL and not resname NA and not resname CL" as a selection that doesn't show popc, water, and ions, for example. I haven't had issues with VMD confusing what a protein is or not, so maybe there is a residue ordering issue or something going on with the gro file? On 2012-09-21 11:19:51PM -0700, Shima Arasteh wrote: > > > Hi, > In order to see a system of protein and lipids, I use VMD. I called > system.gro something similar to what is produced in KALP15 in DPPC. When I > load system.gro and select protein, one of lipids is loaded with it. > I am wondering if it is a problem with my system.gro? Or something with the > applied visualization tool? > > Thanks in advance. > > Sincerely, > Shima > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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 -- 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
