[gmx-developers] lib_search_file_in_dirend called while the 'dirent' functionality is not available on this system

Alexey Shvetsov alexxyum at gmail.com
Wed Feb 17 22:16:16 CET 2010

	Hi all!
I'm trying to use pdb2gmx from git gromacs build and i get this error. Is this 
supposed behavior? Looks like a bug in configure (HAVE_DIRENT_H not checked via 
configure but only checked via cmake) 
grep HAVE_DIRENT  /usr/portage/distfiles/git-src/gromacs/* -R
src/gromacs/CMakeLists.txt:check_include_files(dirent.h     HAVE_DIRENT_H)
/usr/portage/distfiles/git-src/gromacs/src/kernel/fflibutil.c:#ifndef HAVE_DIRENT
/usr/portage/distfiles/git-src/gromacs/src/kernel/fflibutil.c:#ifndef HAVE_DIRENT

                         :-)  G  R  O  M  A  C  S  (-:                                                                                     

                   Great Red Oystrich Makes All Chemists Sane

                 :-)  VERSION 4.0.99_development_20090927  (-:

      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.    

                      :-)  pdb2gmx (double precision)  (-:

Option     Filename  Type         Description
  -f      KT158.pdb  Input        Structure file: gro g96 pdb tpr etc.
  -o      KT158.gro  Output       Structure file: gro g96 pdb etc.    
  -p      KT158.top  Output       Topology file                       
  -i      posre.itp  Output       Include file for topology           
  -n      clean.ndx  Output, Opt. Index file                          
  -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.    

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit  
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel          
-[no]rtpo    bool   no      Allow an entry in a local rtp file to override a
                            library rtp entry                               
-[no]merge   bool   no      Merge chains into one molecule definition       
-ff          string select  Force field, interactive by default. Use -h for 
-water       enum   spc     Water model to use: with GROMOS we recommend SPC,
                            with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p 
                            or f3c                                           
-[no]inter   bool   no      Set the next 8 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]arg     bool   no      Interactive Arganine selection, iso charged      
-[no]asp     bool   no      Interactive Aspartic Acid selection, iso charged 
-[no]glu     bool   no      Interactive Glutamic Acid selection, iso charged 
-[no]gln     bool   no      Interactive Glutamine selection, iso neutral     
-[no]his     bool   no      Interactive Histidine selection, iso checking    
-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   yes     Ignore hydrogen atoms that are in the pdb file   
-[no]missing bool   no      Continue when atoms are missing, dangerous       
-[no]v       bool   no      Be slightly more verbose in messages             
-posrefc     real   1000    Force constant for position restraints           
-vsite       enum   none    Convert atoms to virtual sites: none, hydrogens  
                            or aromatics                                     
-[no]heavyh  bool   no      Make hydrogen atoms heavy                        
-[no]deuterate bool no      Change the mass of hydrogens to 2 amu            
-[no]chargegrp bool yes     Use charge groups in the rtp file                
-[no]cmap    bool   yes     Use cmap torsions (if enabled in the rtp file)   
-[no]renum   bool   no      Renumber the residues consecutively in the output

Program pdb2gmx, VERSION 4.0.99_development_20090927   
Source code file: /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/fflibutil.c, line: 300

Fatal error:
lib_search_file_in_dirend called while the 'dirent' functionality is not 
available on this system
For more information and tips for trouble shooting please check the GROMACS 
website at           

Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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