Hi Justin Could u suggest me which step to carry on further. In place of inflategro , can we use g_membed.
Regards Bhavaniprasad -----Original Message----- From: Justin Lemkul Sent: 3 Aug 2012 10:54:49 GMT To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology On 8/3/12 12:32 AM, Bhavaniprasad.V wrote: > hi justin, > > the problem is actually InflateGro is not deleting any lipids. > I had inserted the protein in lipid using VMD and saved the coordinate file > and > using that directly to this step > > cat pro_in_pope.gro pope_whole.gro > system.gro > > after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5 > area.dat. > Argument "P8" isn't numeric in printf at inflategro.pl line 708. > Argument "O9" isn't numeric in printf at inflategro.pl line 708. > > Calculating Area per lipid... > Protein X-min/max: -4 103 > Protein Y-min/max: -14 100 > X-range: 107 A Y-range: 114 A > Building 107 X 114 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD.... > lower TMD.... > Area per protein: 107.75 nm^2 > Area per lipid: 8.02906194817911 nm^2 > > Area per protein, upper half: 101.25 nm^2 > Area per lipid, upper leaflet : 8.09202321149701 nm^2 > > Area per protein, lower half: 102.25 nm^2 > Area per lipid, lower leaflet : 8.03790402571429 nm^2 > > Writing Area per lipid... > Done! > > So please suggest me what is going wrong > The errors above indicate something is going wrong with printing the output, but from looking at the code I see no reason why this should come up. It is also quite possible that no lipids need to be deleted based on the inflated structure. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
