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

[Alexey Shvetsov]

	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
/usr/portage/distfiles/git-
src/gromacs/CMakeLists.txt:check_include_files(dirent.h     HAVE_DIRENT_H)
/usr/portage/distfiles/git-src/gromacs/src/kernel/fflibutil.c:#ifdef 
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 
                            information.                                    
-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    
                            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   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           
http://www.gromacs.org/Documentation/Errors                                                      
-------------------------------------------------------                                          

-- 
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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