[gmx-users] Re: pdb2gmx file error

[Justin A. Lemkul]

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 /<jalemkul at vt.edu>/* a 
> écrit :
> 
> 
>     De: Justin A. Lemkul <jalemkul at vt.edu>
>     Objet: Re: [gmx-users] Failing installation with --enable-mpi option
>     À: "Discussion list for GROMACS users" <gmx-users at 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:
>      >
>      > [sandaka at 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

========================================