Last login: Tue Nov 30 16:10:40 on ttyp3 Welcome to Darwin! [mriv209-01:~] bo% setenv PATH /Users/bo/gromacs/powerpc-apple-darwin7.6.0/bin [mriv209-01:~] bo% pdb2gmx -f n62.pdb -o n62.gro -p n62.top :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description ------------------------------------------------------------ -f n62.pdb Input Generic structure: gro g96 pdb tpr tpb tpa xml -o n62.gro Output Generic structure: gro g96 pdb xml -p n62.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]merge bool no Merge multiple chains into one molecule -ff string select Force field, interactive by default. Use -h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignh bool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -posrefc real 1000 Force constant for position restraints -dummy enum none Convert atoms to dummy atoms: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /Users/bo/gromacs/share/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 Forcefield (official distribution) 1: GROMOS96 43b1 Vacuum Forcefield (official distribution) 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 4: Gromacs Forcefield (see manual) 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs) 0 Looking whether force field file ffG43a1.rtp exists Opening library file /Users/bo/gromacs/share/top/ffG43a1.rtp Opening library file /Users/bo/gromacs/share/top/aminoacids.dat Reading n62.pdb... Read '?', 1679 atoms Opening library file /Users/bo/gromacs/share/top/xlateat.dat 23 out of 23 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 214 residues with 1679 atoms chain #res #atoms 1 ' ' 214 1679 All occupancies are one Opening library file /Users/bo/gromacs/share/top/ffG43a1.atp Atomtype 50 Reading residue database... (ffG43a1) Opening library file /Users/bo/gromacs/share/top/ffG43a1.rtp Residue 96 Sorting it all out... Opening library file /Users/bo/gromacs/share/top/ffG43a1.hdb Opening library file /Users/bo/gromacs/share/top/ffG43a1-n.tdb Opening library file /Users/bo/gromacs/share/top/ffG43a1-c.tdb Processing chain 1 (1679 atoms, 214 residues) Opening library file /Users/bo/gromacs/share/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: HIS102 CYS123 CYS131 HIS154 CYS158 HIS162 HIS204 NE2825 SG976 SG1035 NE21209 SG1233 NE21266 NE21594 CYS123 SG976 2.111 CYS131 SG1035 2.721 1.339 HIS154 NE21209 1.206 1.622 2.082 CYS158 SG1233 2.144 1.004 1.198 1.159 HIS162 NE21266 2.862 1.531 0.961 1.868 0.811 HIS204 NE21594 2.134 2.822 2.384 1.716 2.159 2.333 HIS212 NE21666 2.785 2.463 1.445 2.487 2.195 2.049 1.780 There are 319 donors and 317 acceptors There are 470 hydrogen bonds Will use HISB for residue 102 Will use HISB for residue 154 Will use HISB for residue 162 Will use HISB for residue 204 Will use HISB for residue 212 Checking for duplicate atoms.... deleting duplicate atom O ALA 214 pdb nr 1679 Now there are 1678 atoms N-terminus: NH3+ C-terminus: COO- Now there are 214 residues with 2120 atoms Making bonds... Opening library file /Users/bo/gromacs/share/top/aminoacids.dat Number of bonds was 2155, now 2150 Generating angles, dihedrals and pairs... Before cleaning: 3554 pairs Before cleaning: 4001 dihedrals There are 1174 dihedrals, 1004 impropers, 3121 angles 3554 pairs, 2150 bonds and 0 dummies Total mass 23951.626 a.m.u. Total charge -2.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have succesfully generated a topology from: n62.pdb. The select force field and the spc water model are used. Note that the default mechanism for selecting a force fields has changed, starting from GROMACS version 3.2.0 --------- ETON ESAELP ------------ gcq#296: "'Nay. We are but men.' Rock!" (Tenacious D) [mriv209-01:~] bo% editconf -f n62.gro -o n62.gro -d 0.5 >& ! out.genbox [mriv209-01:~] bo% genbox -cp n62.gro -cs -o n62.gro -p n62.top >>& ! out.genbox [mriv209-01:~] bo% vi em.mdp tcsh: vi: Command not found. [mriv209-01:~] bo% grompp -f em -c n62 -p n62 -o em1 :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------ -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c n62.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p n62.top Input Topology file -pp processed.top Output, Opt. Topology file -o em1.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmdumbds bool yes Remove constant bonded interactions with dummies -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... sh: line 1: /lib/cpp: No such file or directory cpp exit code: 32512 Tried to execute: '/lib/cpp -I/Users/bo/gromacs/share/top -DFLEX_SPC n62.top > grompp4HvAYT' The '/lib/cpp' command is defined in the .mdp file processing topology... processing coordinates... Fatal error: number of coordinates in coordinate file (n62.gro, 17981) does not match topology (n62.top, 0) [mriv209-01:~] bo%