Hi kayal, Well, given that it reads "Fatal error" your final question seems a bit odd, doesn't it? How did you obtain the topology? Apparently, there's a bit more specified in it than a single butane! Besides, I notice that you use the GROMOS force field, which is a united atom force field. That means that aliphatic hydrogens are collapsed onto the bearing C atoms. Ergo, butane in a UA force field will count exactly four atoms. But you have thirteen in your coordinate file. Maybe it would be a good idea to read up a bit on the background of MD: force fields, topologies, etc. Most tutorials, although commonly aimed at proteins, will introduce these concepts and give you a feel for the matter.
Tsjerk On Thu, Aug 27, 2009 at 1:20 PM, abhijit kayal<[email protected]> wrote: > Hi, > I am going to analyse the normal mode analysis of n-butane. For this I > donloaded a PDB id .Then opened in wordpad and just took the glu > residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make > it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created > the topology file and did the next steps .But grompp showed the following > error > abhi...@scfbioserver project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o > ab.tp > r > :-) G R O M A C S (-: > GROwing Monsters And Cloning Shrimps > :-) VERSION 4.0.4 (-: > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, 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 ab.gro Input Structure file: gro g96 pdb tpr tpb tpa > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -n index.ndx Input, Opt. Index file > -p ab.top Input Topology file > -pp processed.top Output, Opt. Topology file > -o ab.tpr Output Run input file: tpr tpb tpa > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt > -e ener.edr Input, Opt. Energy file: 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. > -[no]rmvsbds bool yes Remove constant bonded interactions with virtual > sites > -maxwarn int 0 Number of allowed warnings during input > processing > -[no]zero bool no Set parameters for bonded interactions without > defaults to zero instead of generating an error > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > Ignoring obsolete mdp entry 'cpp' > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9# > checking input for internal consistency... > processing topology... > Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp > Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp > Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp > Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp > Generated 380 of the 1326 non-bonded parameter combinations > Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp > Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp > Excluding 3 bonded neighbours molecule type 'Protein_A' > Excluding 2 bonded neighbours molecule type 'SOL' > Excluding 2 bonded neighbours molecule type 'SOL' > NOTE 1 [file ab.top, line 126]: > System has non-zero total charge: -1.000000e-00 > > processing coordinates... > ------------------------------------------------------- > Program grompp, VERSION 4.0.4 > Source code file: grompp.c, line: 362 > Fatal error: > number of coordinates in coordinate file (ab.gro, 13) > does not match topology (ab.top, 29602) > ------------------------------------------------------- > "A Lady Shaves Her Legs" (C. Meijering) > So my questioin is my way of procedding is > wrong or right? > > _______________________________________________ > 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]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
