[gmx-users] oplsff- need of gro and itp file -reg
Respected gromacs people's, for protein and ligand complex i want use opls ff, here found mktop for ligand (external tool in gromacs web-page) but it only provide topology file only,my question is were i will get the .gro file and .itp file ? Thank You -- Regards,* *S.VENKATESH, -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_covar -reg
Respected Sir / Madam i did temperature study for that i need analysis principal component analysis so, i followed GROMACS Introductory Tutorial (4.5.5) *g_covar* g_covar -s md_0_2.tpr -f md_merged_20_ns.xtc -o 2KW8_275_eigenval.xvg -v 2KW8_275_eigenvect.trr -xpma 2KW8_275_covara.xpm Choose a group for the least squares fit: 4(Backbone) Choose a group for the least squares fit: 4(Backbone) *xpm2ps* xpm2ps -f 2KW8_275_covara.xpm -o 2KW8_275_covara.eps -do covara.m2p in all my result nothing is there visualize, color is very poor to understand what can i do? kindly give me prompt answer Thanking You In Advance -- *S.VENKATESH* -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_sas doubt -reg
Dear Sir / Madam, I want run Solvent accessible surface area in gromacs,i aware about g_sas is there but for selecting group little bit confusing Reading frame 0 time0.000 Select a group for calculation of surface and a group for output: Group 0 ( System) has 210538 elements Group 1 (Protein) has 1517 elements Group 2 ( Protein-H) has 1199 elements Group 3 (C-alpha) has 158 elements Group 4 ( Backbone) has 474 elements Group 5 ( MainChain) has 633 elements Group 6 ( MainChain+Cb) has 779 elements Group 7 (MainChain+H) has 789 elements Group 8 ( SideChain) has 728 elements Group 9 (SideChain-H) has 566 elements Group10 (Prot-Masses) has 1517 elements Group11 (non-Protein) has 209021 elements Group12 ( Other) has 6200 elements Group13 ( DPPC) has 6200 elements Group14 ( CL) has21 elements Group15 ( Water) has 202800 elements Group16 (SOL) has 202800 elements Group17 ( non-Water) has 7738 elements Group18 (Ion) has21 elements Group19 ( DPPC) has 6200 elements Group20 ( CL) has21 elements Group21 ( Water_and_ions) has 202821 elements Select a group: 1 Selected 1: 'Protein' *Select a group: ? (Which I want Select)* kindly provide answers Thanking You In Advance -- *S.VENKATESH,* Tamil Nadu,India -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs: pdb2gmx error
Thanking you Mark Abraham for your valuable suggestion Here i used DNA Ligand Complex only is that any specific options is there? Thanks -- *S.VENKATESH,* II M.Sc Bioinformatics, Alagappa University, Karaikudi-630003 Tamil Nadu, India svenkateshbioinformat...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs: pdb2gmx error
Hi i got that error in the step of pdb2gmx what can i do i read also http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database can any one tell exact reason and how i handle further thanking you - All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.4# Processing chain 1 'E' (603 atoms, 20 residues) Identified residue DG2 as a starting terminus. Warning: Residue MN1022 in chain has different type (Other) from starting residue DG2 (DNA). Identified residue DT20 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'DG' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- *S.VENKATESH,* II M.Sc Bioinformatics, Alagappa University, Karaikudi-630003 Tamil Nadu, India Mobile Phone:- 9486494616 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs installtion error
hi, I am facing problem:--> installation of gromacs i got that following error (Note: i run the root only, previously i installed fftw ) Kindly any one give me a opt answer /usr/bin/ld: /usr/local/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/student/Desktop/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/student/Desktop/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/student/Desktop/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 Thanks in Advance -- *S.VENKATESH,* II M.Sc Bioinformatics, Alagappa University, Karaikudi-630003 Tamil Nadu, India svenkateshbioinformat...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
