Hi Justin I am trying to prep a pdb file for md but keep on getting this error message
Fatal error: Chain identifier 'O' was used in two non-sequential blocks (residue 2400, atom 18726) Fatal error: But when I look at the file I only have one chain identifier. Also when I strip off hydrogens and run pdb2gmx again this is the error I get Fatal error: Atom CB not found in residue VAL20 while adding hydrogens I donot understand why and would appreciate some help Thanks Dadado --- En date de : Mer 20.5.09, Justin A. Lemkul <jalem...@vt.edu> a écrit : De: Justin A. Lemkul <jalem...@vt.edu> Objet: Re: [gmx-users] Failing installation with --enable-mpi option À: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Mercredi 20 Mai 2009, 14h01 Bhanu wrote: > I tried to install Gromacs on my Core2Quad pc with the command > > ./configure --enable-mpi --disable-nice --program-suffix="_mpi" > > it is showing the following error result: > > [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice > --program > -suffix="_mpi" > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > /bin/sh: /home/sandaka/Desktop/all: No such file or directory > configure: WARNING: `missing' script is too old or missing > checking for a thread-safe mkdir -p... /bin/mkdir -p > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking how to create a ustar tar archive... gnutar > checking for cc... cc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether cc accepts -g... yes > checking for cc option to accept ISO C89... none needed > checking for style of include used by make... GNU > checking dependency style of cc... gcc3 > checking dependency style of cc... gcc3 > checking for mpxlc... no > checking for mpicc... mpicc > checking whether the MPI cc command works... yes > checking for catamount... no > checking how to run the C preprocessor... mpicc -E > checking whether mpicc accepts -O3... yes > checking whether mpicc accepts -funroll-all-loops... yes > checking whether mpicc accepts -O3 -fomit-frame-pointer > -finline-functions -Wall -Wno-unused -funroll-all-loops... yes > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... no > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking whether byte ordering is bigendian... no > checking for int... yes > checking size of int... configure: error: cannot compute sizeof (int) > See `config.log' for more details. > > Am attaching the config.log file herein. I've Openmpi and fftw already > installed and in the path.. Couldn't understand what is the error! > > Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php