Hello Justin tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr
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 39 ( EMI) has 2432 elements Group 40 ( C) has 128 elements --- ---- Group 57 ( H18) has 128 elements Group 58 ( H19) has 128 elements Group 59 ( CL) has 128 elements Group 60 ( CL) has 128 elements I selected Group 0 After this I followed the steps given in g_spatial -h. I selected residue Group 14 and EMI is Group 39 for trjconv. 1. trjconv -s test.tpr -f 3.xtc -o b.xtc -center -ur compact -pbc none -n glu-emi-cl-128-no.ndx 2. trjconv -s test.tpr -f b.xtc -o c.xtc -fit rot+trans -n glu-emi-cl-128-no.ndx For 2nd step I got the error Fatal error: Index[2385] 2410 is larger than the number of atoms in the trajectory file (2409). As I want to plot how glucose (GLU:Group 14 )is surrounded by cation (EMI:Group 39). Should I select Group 14 in tpbconv ? Sorry for so much details and your help is really appreciated. Thanks Nilesh On Wed, May 12, 2010 10:58 am, [email protected] wrote: > > Hi Nilesh, > If you need the whole system you maybe don't need to include the -n flag > in the tpbconv command it will still create your new tpr file for > continuing your work without errors, I had earlier some similar problem. > But as Justin mentioned it is due to some specification in the mpd as for > part of your system was selected only.. Gigi > > > > > > > > > > -----E-mail d'origine----- > De : Nilesh Dhumal <[email protected]> > A : [email protected]; Discussion list for GROMACS users > <[email protected]> > Envoyé le : Mercredi, 12 Mai 2010 17:47 > Sujet : Re: [gmx-users] trjconv : error > > > > Hello Justin, > As you suggest I used tbpconv > > > tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr > and I selected group 0 for system group (In system group all atoms are > present.) > > Still I am getting the same error. > > > > I have one more question, > I am working on solvation glucose in ionic liquids. As I told you I want > to show glucose surrounded by cation using iso-surface. After loading > grid.cub file in vmd, all atoms are present. How can I do sothat I can > get only glucose and plot the iso-surface to show cation position. Can you > help me to solve this problem. > > Thanks > Nilesh > > > On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote: > >> > >> >> Nilesh Dhumal wrote: >> >> >>> Hello, >>> I am trying to calculate spatial distribution function (SDF) for my >>> system. >>> >>> 1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none >>> -n >>> test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n >>> test.ndx >>> >>> I am getting the following error for step 2. >>> >>> >>> >>> Fatal error: Index[2385] 2410 is larger than the number of atoms in >>> the trajectory file (2409). >>> >>> How can I solve this problem? >>> Duirng my simulation I didn't specify xtc_grps this option in md >>> file. >>> >>> >> >> Then it looks like you must have saved only a subset of your system >> during step 1 or some other post-processing step. Either save the whole >> system, or use tpbconv to generate a .tpr file that contains only the >> relevant subset of atoms. >> >> -Justin >> >> >> >>> >>> >>> Thanks >>> >>> >>> >>> Nilesh >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> -- >> ======================================== >> >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. 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