Here are details. the first three groups from GUL residue and the last in cation (residue)
Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 ( Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group 10 ( Prot-Masses) has 2456 elements Group 11 ( Non-Protein) has 128 elements Group 12 ( CL) has 128 elements Group 13 ( Other) has 128 elements Group 14 ( GUL) has 24 elements Group 15 ( O) has 1 elements Group 16 ( C2) has 129 elements Group 17 ( C3) has 1 elements Group 18 ( C4) has 129 elements Group 19 ( C5) has 1 elements Group 20 ( C6) has 129 elements -- -- Group 39 ( EMI) has 2432 elements Group 40 ( C) has 128 elements - - Group 58 ( H19) has 128 elements Group 59 ( CL) has 128 elements Group 60 ( CL) has 128 elements Select a group: 16 Selected 16: 'C2' Select a group: 17 Selected 17: 'C3' Select a group: 18 Selected 18: 'C4' Select a group: 39 Selected 39: 'EMI' trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 ------------------------------------------------------- Program g_sdf, VERSION 4.0.5 Source code file: gmx_sdf.c, line: 177 Fatal error: For single particle SDF, all reference groupsmust have the same size. ------------------------------------------------------- Nilesh On Mon, May 17, 2010 8:23 pm, Dallas B. Warren wrote: > Can you copy and paste into here what you see between: > > > "Select a reference group and 1 group" > > > And > > > "Select a group:" > > > When you run the script. > > > Catch ya, > > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble > a nail. > > >> -----Original Message----- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May >> 2010 9:29 AM >> To: Discussion list for GROMACS users >> Subject: RE: [gmx-users] g_sdf : error >> >> >> hey Sorry for typing mistake. >> I used ths command. >> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r >> >> Nilesh >> >> >> On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: >> >>>> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt >>>> >> -r >> >>> >>> Is that the exact command line you used? If so, doubt it would >>> >> actually >>> work, since it should be: >>> >>> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt > - > >> r >>> >>> Catch ya, >>> >>> >>> >>> Dr. Dallas Warren >>> Drug Delivery, Disposition and Dynamics >>> Monash Institute of Pharmaceutical Sciences, Monash University >>> 381 Royal Parade, Parkville VIC 3010 >>> dallas.war...@pharm.monash.edu.au +61 3 9903 9167 >>> --------------------------------- >>> When the only tool you own is a hammer, every problem begins to >>> >> resemble >>> a nail. >>> >>>> -----Original Message----- >>>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >>>> boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 >> May >> >>>> 2010 5:55 AM >>>> To: gmx-users@gromacs.org >>>> Subject: [gmx-users] g_sdf : error >>>> >>>> >>>> >>>> Hello, >>>> I am trying to run g_sdf for sovlation for glucose in ionic >>>> > liquids. >>>> I am trying to find distribution of anion around glucose. >>>> >>>> >>>> >>>> >>>> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt >>>> >> -r >> >>>> >>>> First three group I selected from the same residue (Glucose). Forth >>>> grouup I selected from as anion (Anion residue ). I am geting >> following >>>> >>> error. >>>> >>>> Fatal error: >>>> For single particle SDF, all reference groupsmust have the same >>>> >> size. >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> 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/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/mailing_lists/users.php >>>> >>>> >>> -- >>> 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/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/mailing_lists/users.php >>> >>> >>> >>> >> >> >> -- >> 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/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/mailing_lists/users.php >> > -- > 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/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/mailing_lists/users.php > > > -- 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/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/mailing_lists/users.php
