Hi I tried to run the minimization step . Minimization went on well but am not confout.gro
Is there any specific command for obtaining an confout.gro while running em. Regards -----Original Message----- From: Justin Lemkul Sent: 3 Aug 2012 14:55:25 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 10:52 AM, bhavaniprasad vipperla wrote: > Hi Justin > Could u suggest me which step to carry on further. > It's not clear to me that InflateGRO truly failed, though some of the output is curious, as noted before. > In place of inflategro , can we use g_membed. > Sure. I don't use it personally, but others do. -Justin > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists