[gmx-users] grompp segmentation error

[ram bio]

Dear Justin,

Thanks for the response.

I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have
asked my system admin to provide the details regarding the cluster,
whereas for my PC:

The info is as follows:

1. The Gromacs version you are using. - 4.0.3
2. The compilers used in installing Gromacs.- gcc
gcc -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre
--with-cpu=generic --host=i386-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)

 3. Options specified during configuration.

I didnot get this, can you please elaborate...


4. Specifications of your hardware.

processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 13
model name      : Intel(R) Pentium(R) M processor 1.70GHz
stepping        : 6
cpu MHz         : 600.000
cache size      : 2048 KB
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 2
wp              : yes
flags           : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat
clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2
bogomips        : 1196.53

Linux version 2.6.18-8.el5 (mockbuild at builder4.centos.org) (gcc
version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35
EDT 2007

Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc.
Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1
SMP Thu Mar 15 19:57:35 EDT 2007 i686
Build Date: 21 June 2008
Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1


I would be providing the info about the cluster, once I receive it,
mean please let me know if any info is missing and help me.

Thanks,

Ram





On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Gromacs Users,
>>
>> Iam following Drug/Enzyme complex solvation tutorial by John E.
>> Kerrigan, I am unable to execute the grompp step as per the tutorial,
>> the output of grompp command is as follows:
>>
>> grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr
>>
>>
>>                               :-)  grompp  (-:
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
>> checking input for internal consistency...
>> processing topology...
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
>> Segmentation fault
>>
>> what i have done is as per the tutorial, that is
>> 1) generated the drg.itp using prodrug beta
>> 2) executed pdb2gmx using 4 that is ff53a6 ff
>> 3) edit the drg.itp by removing the lines redundant as per trp.top
>> 4) edit trp.gro by adding drg coordinates and chainging the numbers
>>
>> please help me to overcome this error, for your convenience I have
>> attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files.
>>
>
> I doubt any of these files will be useful.  Better information would
> include:
>
> 1. The Gromacs version you are using.
> 2. The compilers used in installing Gromacs.
> 3. Options specified during configuration.
> 4. Specifications of your hardware.
>
> A segmentation fault is a memory error and can have numerous causes.  The
> above information may be useful.
>
> -Justin
>
>> Thanks,
>>
>> Ram
>> 4 attachments —
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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