Hi Bipin, The file residuetypes.dat is quite different from aminoacids.dat. You can paste the following into that file (first line is number of entries, followed by so many residue names):
49 ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA GLN GLU GLUH GLY HIS HIS1 HISA HISB HISH HYP ILE LEU LYS LYSH MELEU MET MEVAL NAC NH2 PHE PHEH PHEU PHL PRO SER THR TRP TRPH TRPU TYR TYRH TYRU VAL Groetjes, Tsjerk On Mon, Feb 21, 2011 at 8:47 AM, bipin singh <bipinel...@gmail.com> wrote: > Hi, > Thanks for your suggestion. > While running the g_covar it is showing the error that aminoacids.dat is not > found, so i have copied the residuetypes.dat(which i seems the new modified > name for aminoacids.dat in current GROMACS version), then it prompts to > choose the group for least square fit, which is not usual groups(i.e protein > or C alpha groups etc.).....please suggest where i have made mistake. > > Choose a group for the least squares fit > Opening library file aminoacids.dat > WARNING 2 [file aminoacids.dat, line 1]: > File aminoacids.dat is empty > Group 0 ( System) has 30585 elements > Group 1 ( GLU) has 47 elements > Group 2 ( HIS) has 86 elements > Group 3 ( ASN) has 224 elements > Group 4 ( PRO) has 56 elements > Group 5 ( VAL) has 272 elements > Group 6 ( MET) has 68 elements > Group 7 ( GLY) has 168 elements > Group 8 ( ILE) has 190 elements > Group 9 ( ALA) has 110 elements > Group 10 ( SER) has 143 elements > Group 11 ( PHE) has 80 elements > Group 12 ( LYS) has 242 elements > Group 13 ( TYR) has 189 elements > Group 14 ( LEU) has 304 elements > Group 15 ( GLN) has 102 elements > Group 16 ( TRP) has 48 elements > Group 17 ( ARG) has 120 elements > Group 18 ( ASP) has 108 elements > Group 19 ( THR) has 141 elements > Group 20 ( SOL) has 27882 elements > Group 21 ( CL) has 5 elements > > > On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> >> Hi Bipin, >> >> Try using a .gro or .pdb file as reference structure (-s). Only .tpr files >> are version specific. >> >> Cheers, >> >> Tsjerk >> >> On Feb 21, 2011 8:05 AM, "bipin singh" <bipinel...@gmail.com> wrote: >> >> Dear GMX users, >> >> I want to calculate the correlated motion between atoms during the md >> simulation >> >> for that purpose I am using g_covar(the one which is available under >> http://www.gromacs.org/Downloads/User_contributions/Other_software) >> >> >> >> but it is not compatible with the GROMACS-4.5.3, so please suggest me the >> alternative way or does anyone have the modified g_covar for >> GROMKACS-4.5.3. >> >> -- >> --------------------------------- >> Thanks and regards >> Bipin Singh >> >> >> -- >> gmx-users mailing list gmx-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 mailing list gmx-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 > > > > -- > --------------------------------- > Thanks and regards > Bipin Singh > > > -- > gmx-users mailing list gmx-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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-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