<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Justin<br>I am trying to prep a pdb file for md but keep on getting this error message<br><br>Fatal error:<br>Chain identifier 'O' was used in two non-sequential blocks (residue 2400, atom 18726)<br>Fatal error:<br><br>But when I look at the file I only have one chain identifier.<br><br>Also when I strip off hydrogens and run pdb2gmx again this is the error I get<br>Fatal error:<br>Atom CB not found in residue VAL20 while adding hydrogens<br><br>I donot understand why and would appreciate some help<br><br>Thanks<br>Dadado<br><br><br>--- En date de : <b>Mer 20.5.09, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> a écrit :<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>De: Justin A. Lemkul <jalemkul@vt.edu><br>Objet: Re: [gmx-users] Failing installation with --enable-mpi
option<br>À: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Mercredi 20 Mai 2009, 14h01<br><br><div class="plainMail"><br><br>Bhanu wrote:<br>> I tried to install Gromacs on my Core2Quad pc with the command<br>> <br>> ./configure --enable-mpi --disable-nice --program-suffix="_mpi"<br>> <br>> it is showing the following error result:<br>> <br>> [sandaka@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program<br>> -suffix="_mpi"<br>> checking build system type... i686-pc-linux-gnu<br>> checking host system type... i686-pc-linux-gnu<br>> checking for a BSD-compatible install... /usr/bin/install -c<br>> checking whether build environment is sane... yes<br>> /bin/sh: /home/sandaka/Desktop/all: No such file or directory<br>> configure: WARNING: `missing' script is too old or missing<br>> checking for a thread-safe mkdir -p... /bin/mkdir -p<br>> checking for
gawk... gawk<br>> checking whether make sets $(MAKE)... yes<br>> checking how to create a ustar tar archive... gnutar<br>> checking for cc... cc<br>> checking for C compiler default output file name... a.out<br>> checking whether the C compiler works... yes<br>> checking whether we are cross compiling... no<br>> checking for suffix of executables...<br>> checking for suffix of object files... o<br>> checking whether we are using the GNU C compiler... yes<br>> checking whether cc accepts -g... yes<br>> checking for cc option to accept ISO C89... none needed<br>> checking for style of include used by make... GNU<br>> checking dependency style of cc... gcc3<br>> checking dependency style of cc... gcc3<br>> checking for mpxlc... no<br>> checking for mpicc... mpicc<br>> checking whether the MPI cc command works... yes<br>> checking for catamount... no<br>> checking how to run the C preprocessor...
mpicc -E<br>> checking whether mpicc accepts -O3... yes<br>> checking whether mpicc accepts -funroll-all-loops... yes<br>> checking whether mpicc accepts -O3 -fomit-frame-pointer<br>> -finline-functions -Wall -Wno-unused -funroll-all-loops... yes<br>> checking for grep that handles long lines and -e... /bin/grep<br>> checking for egrep... /bin/grep -E<br>> checking for ANSI C header files... no<br>> checking for sys/types.h... yes<br>> checking for sys/stat.h... yes<br>> checking for stdlib.h... yes<br>> checking for string.h... yes<br>> checking for memory.h... yes<br>> checking for strings.h... yes<br>> checking for inttypes.h... yes<br>> checking for stdint.h... yes<br>> checking for unistd.h... yes<br>> checking whether byte ordering is bigendian... no<br>> checking for int... yes<br>> checking size of int... configure: error: cannot compute sizeof (int)<br>> See `config.log' for more
details.<br>> <br>> Am attaching the config.log file herein. I've Openmpi and fftw already<br>> installed and in the path.. Couldn't understand what is the error!<br>> <br>> <br><br>Have a look at this thread:<br><br><a href="http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html</a><br><br>-Justin<br><br>> <br>> <br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a
href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php"
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