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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>The eigenvector file is only stored in .trr format for coding convenience.<br>It was never intended to be used with trjconv etc.<br>But if you want to use it that way you indeed have to use editconf<br>to make a structure file with only the atoms you used in the analysis,<br>as you did.<br></div><br>I don't know why you want to write the eigenvectors to pdb.<br>They will not give you meaningful structures.<br><br>g_anaeig has several options to visualize eigenvectors.<br><br>Berk.<br><br><hr id="stopSpelling">> Date: Thu, 24 Jul 2008 15:49:56 -0400<br>> From: mldaniel@pharmacy.purdue.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Possible Bug????<br>> <br>> Users,<br>> I am having a problem when trying to convert a .trr to a .pdb using <br>> trjconv. I think there could there be a bug in the program and the <br>> index group is getting confused. Here is exactly what i am doing:<br>> Command:<br>> trjconv -f eigenvec.trr -s prot_md.gro -o test.pdb<br>> Output:<br>> Will write pdb: Protein data bank file<br>> Select group for output<br>> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>> Group 0 ( System) has 68361 elements<br>> Group 1 ( Protein) has 7588 elements<br>> Group 2 ( Protein-H) has 3780 elements<br>> Group 3 ( C-alpha) has 467 elements<br>> Group 4 ( Backbone) has 1401 elements<br>> Group 5 ( MainChain) has 1867 elements<br>> Group 6 (MainChain+Cb) has 2307 elements<br>> Group 7 ( MainChain+H) has 2305 elements<br>> Group 8 ( SideChain) has 5283 elements<br>> Group 9 ( SideChain-H) has 1913 elements<br>> Group 10 ( Prot-Masses) has 7588 elements<br>> Group 11 ( Non-Protein) has 60773 elements<br>> Group 12 ( FLP) has 30 elements<br>> Group 13 ( SOL) has 60741 elements<br>> Group 14 ( Cl) has 2 elements<br>> Group 15 ( Other) has 60773 elements<br>> Select a group: 4<br>> Selected 4: 'Backbone'<br>> trn version: GMX_trn_file (single precision)<br>> Reading frame 0 time 0.000<br>> Back Off! I just backed up test.pdb to ./#test.pdb.1#<br>> <br>> -------------------------------------------------------<br>> Program trjconv, VERSION 3.3.2<br>> Source code file: gmx_trjconv.c, line: 994<br>> <br>> Fatal error:<br>> Index[267] 1403 is larger than the number of atoms in the trajectory <br>> file (1401)<br>> -------------------------------------------------------<br>> <br>> I have been able to get around this problem (really only a work around <br>> this bug). Here is what i have done:<br>> editconf -f prot_md.gro -o eigenvec_base.gro -n index.ndx<br>> output only the Backbone atoms, and then run trjconv with the output <br>> from editconf as the template file (-s file). This then will translate <br>> the .trr file to a .pdb.<br>> <br>> Has anyone else seen this, or have any ideas???<br>> Thanks!<br>> -- <br>> <br>> Matthew L. Danielson<br>> <br>> Graduate Student of Medicinal Chemistry & Molecular Pharmacology<br>> College of Pharmacy, Nursing, and Health Sciences<br>> Purdue University<br>> MCMP RHPH 516<br>> 575 Stadium Mall Drive<br>> West Lafayette, IN 47907-2091<br>> <br>> (765)494-6564 office<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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