hello every one i am working on complex with popc membrane i got error in Deuterium Order Parameters group 1 does not have same number of elements as grp 1 i used the command
make_ndx -f md_0_1.tpr -o sn1.ndx 0 System : 38483 atoms 1 Protein : 3873 atoms 2 Protein-H : 3061 atoms 3 C-alpha : 408 atoms 4 Backbone : 1224 atoms 5 MainChain : 1633 atoms 6 MainChain+Cb : 2015 atoms 7 MainChain+H : 2000 atoms 8 SideChain : 1873 atoms 9 SideChain-H : 1428 atoms 10 Prot-Masses : 3873 atoms 11 non-Protein : 34610 atoms 12 Other : 6365 atoms 13 UNK : 21 atoms 14 POPC : 6344 atoms 15 CL : 15 atoms 16 Water : 28230 atoms 17 SOL : 28230 atoms 18 non-Water : 10253 atoms 19 Ion : 15 atoms 20 UNK : 21 atoms 21 POPC : 6344 atoms 22 CL : 15 atoms 23 Water_and_ions : 28245 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > aC34 Found 122 atoms with name C34 24 C34 : 122 atoms > aC36 Found 122 atoms with name C36 25 C36 : 122 atoms > a C37 Found 122 atoms with name C37 26 C37 : 122 atoms > a C38 Found 122 atoms with name C38 27 C38 : 122 atoms > a C39 Found 122 atoms with name C39 28 C39 : 122 atoms > a C40 Found 122 atoms with name C40 29 C40 : 122 atoms > a C41 Found 122 atoms with name C41 30 C41 : 122 atoms > a C42 Found 122 atoms with name C42 31 C42 : 122 atoms > A C43 Syntax error: "A C43" > a C43 Found 122 atoms with name C43 32 C43 : 122 atoms > a C44 Found 122 atoms with name C44 33 C44 : 122 atoms > a C45 Found 122 atoms with name C45 34 C45 : 122 atoms > a C46 Found 122 atoms with name C46 35 C46 : 122 atoms > a C47 Found 122 atoms with name C47 36 C47 : 122 atoms > a C48 Found 122 atoms with name C48 37 C48 : 122 atoms > a C49 Found 122 atoms with name C49 38 C49 : 122 atoms > a C50 Found 122 atoms with name C50 39 C50 : 122 atoms > a CA1 Found 122 atoms with name CA1 40 CA1 : 122 atoms > a CA2 Found 122 atoms with name CA2 41 CA2 : 122 atoms > del 0-21 Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'non-Protein' Removed group 12 'Other' Removed group 13 'UNK' Removed group 14 'POPC' Removed group 15 'CL' Removed group 16 'Water' Removed group 17 'SOL' Removed group 18 'non-Water' Removed group 19 'Ion' Removed group 20 'UNK' Removed group 21 'POPC' > q 0 System : 38483 atoms 1 Protein : 3873 atoms 2 Protein-H : 3061 atoms 3 C-alpha : 408 atoms 4 Backbone : 1224 atoms 5 MainChain : 1633 atoms 6 MainChain+Cb : 2015 atoms 7 MainChain+H : 2000 atoms 8 SideChain : 1873 atoms 9 SideChain-H : 1428 atoms 10 Prot-Masses : 3873 atoms 11 non-Protein : 34610 atoms 12 Other : 6365 atoms 13 UNK : 21 atoms 14 POPC : 6344 atoms 15 CL : 15 atoms 16 Water : 28230 atoms 17 SOL : 28230 atoms 18 non-Water : 10253 atoms 19 Ion : 15 atoms 20 UNK : 21 atoms 21 POPC : 6344 atoms 22 CL : 15 atoms 23 Water_and_ions : 28245 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > a C15 Found 122 atoms with name C15 24 C15 : 122 atoms > a C17 Found 122 atoms with name C17 25 C17 : 122 atoms > a C18 Found 122 atoms with name C18 26 C18 : 122 atoms > a C19 Found 122 atoms with name C19 27 C19 : 122 atoms > a C20 Found 122 atoms with name C20 28 C20 : 122 atoms > a C21 Found 122 atoms with name C21 29 C21 : 122 atoms > a C22 Found 122 atoms with name C22 30 C22 : 122 atoms > a C23 Found 122 atoms with name C23 31 C23 : 122 atoms > a C24 Found 122 atoms with name C24 32 C24 : 122 atoms > a C25 Found 122 atoms with name C25 33 C25 : 122 atoms > a C26 Found 122 atoms with name C26 34 C26 : 122 atoms > a C27 Found 122 atoms with name C27 35 C27 : 122 atoms > a C28 Found 122 atoms with name C28 36 C28 : 122 atoms > a C29 Found 122 atoms with name C29 37 C29 : 122 atoms > a C30 Found 122 atoms with name C30 38 C30 : 122 atoms > a C31 Found 122 atoms with name C31 39 C31 : 122 atoms > q mtechbio@mtechbio-HP-Z400-Workstation:~/Desktop/pt1/pt1/epi$ g_order_d -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg Taking z axis as normal to the membrane Reading file md_0_1.tpr, VERSION 4.5.5 (single precision) Using following groups: Groupname: CL First atomname: CL First atomnr 38468 Groupname: Water_and_ions First atomname: OW First atomnr 10238 Groupname: C34 First atomname: C34 First atomnr 3927 Groupname: C36 First atomname: C36 First atomnr 3929 Groupname: C37 First atomname: C37 First atomnr 3930 Groupname: C38 First atomname: C38 First atomnr 3931 Groupname: C39 First atomname: C39 First atomnr 3932 Groupname: C40 First atomname: C40 First atomnr 3933 Groupname: C41 First atomname: C41 First atomnr 3934 Groupname: C42 First atomname: C42 First atomnr 3935 Groupname: C43 First atomname: C43 First atomnr 3936 Groupname: C44 First atomname: C44 First atomnr 3937 Groupname: C45 First atomname: C45 First atomnr 3938 Groupname: C46 First atomname: C46 First atomnr 3939 Groupname: C47 First atomname: C47 First atomnr 3940 Groupname: C48 First atomname: C48 First atomnr 3941 Groupname: C49 First atomname: C49 First atomnr 3942 Groupname: C50 First atomname: C50 First atomnr 3943 Groupname: CA1 First atomname: CA1 First atomnr 3944 Groupname: CA2 First atomname: CA2 First atomnr 3945 Reading frame 0 time 0.000 Number of elements in first group: 15 ------------------------------------------------------- Program g_order_d, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/gmx_order.c, line: 489 Fatal error: grp 1 does not have same number of elements as grp 1 kindly help i didnt get the Dallas Warner post On Mon, Jul 28, 2014 at 5:24 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/28/14, 1:42 AM, RINU KHATTRI wrote: >> >> hello everyone >> >> i used editconf >> >> editconf -f protein.gro -o protein_newbox.gro -box (membrane box >> vectors) -center *x y z* >> >> >> but in z axis i have been increased box size 10.0000 (previously it is >> 6.23910 6.17970 6.91950 >> >> http://s48.photobucket.com/user/mittukhattri/media/ri_zpsbb51fbd7.png.html?filters[user]=140927090&filters[recent]=1&sort=1&o=0 >> >> this is the em.gro first minimization image >> >> mixing of lipid and protein molecule >> >> kindly help >> > > I don't see any evidence of a problem. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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