Thanks. Its working. Why all coordinates are zero in refmol.gro file. NIlesh
On Mon, May 17, 2010 9:31 pm, Dallas B. Warren wrote: > As I suspected: > > > Group 16 ( C2) has 129 elements > Group 17 ( C3) has 1 elements > Group 18 ( C4) has 129 elements > > > As the error has told you, C3 does not have the same number of elements > as C2 and C4. > > 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 11:21 AM >> To: Discussion list for GROMACS users >> Subject: RE: [gmx-users] g_sdf : error >> >> >> 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 >> > -- > 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
