Please keep all Gromacs-related correspondence on the gmx-users list; I do not
advertise as a free tutor :)
yimnai forlemu wrote:
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.
Then something is either incorrectly formatted, or you are not finding the real
problem. Look at the line pdb2gmx is pointing to, and see here:
http://wiki.gromacs.org/index.php/Errors#Chain_identifier_.27X.27_was_used_in_two_non-sequential_blocks
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
You have a broken structure. Check the header of the .pdb file for MISSING
entries. Also, refer here:
http://wiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms
Most errors that new users face can be found in wiki entries, or by searching
the list archive.
-Justin
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
>
>
>
>
>
------------------------------------------------------------------------
>
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-- ========================================
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
========================================
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--
========================================
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
========================================
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