[gmx-users] pdb2gmx file error

[yimnai forlemu]

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 <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

> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090520/5c137b02/attachment.html>