[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

[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

[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 (

[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

[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

[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