Re: [gmx-users] grompp segmentation error
Dear Justin, I am having grompp segmentation error only for the drug-enzyme complex tutorial, all other executables are ok, can this occur due to the any other reasons like following the tutorial improperly. Thanks, Ram On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the response. >> >> Here is the info regarding the cluster where gromacs version 4.0.5 is >> installed with icc compliers. >> >> $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 >> uname -m = x86_64 >> uname -r = 2.6.18-128.7.1.el5 >> uname -s = Linux >> uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 >> compilers: C and fortran Intel 10.1 >> >> Please suggest me as the grompp command also donot work with this >> configuration. > > Does grompp give any other output, or does it just seg fault? Do other > executables work on this system? > > There are a whole host of issues that could be causing this, from 32/64 bit > mismatch, shared libraries being moved, etc, so it is very difficult to > diagnose. Was the whole package compiled with MPI (per the above command)? > If so, there is no point, since the only MPI-enabled executable is mdrun. > It may help to re-compile correctly if this is the case (a bit of a long > shot, but perhaps worth trying). Do you have gcc available on the cluster, > to test and see if it produces functioning code? > > -Justin > >> >> Thanks, >> >> Ram >> >> On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul wrote: >>> >>> ram bio wrote: 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) >>> The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs >>> source code download site: >>> >>> "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. >>> These >>> compilers come with recent Linux distrubutions like Fedora 5/6 etc." >>> >>> I would suggest updating to the latest version of Gromacs (4.0.7), using >>> a >>> more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and >>> 4.2.x and newer, are fine). >>> 3. Options specified during configuration. I didnot get this, can you please elaborate... >>> Things like --enable-shared, --disable-(whatever), but I don't know that >>> any >>> of this is relevant. I think the compiler is the problem. >>> >>> -Justin >>> 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 (mockbu...@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 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: >>>
Re: [gmx-users] grompp segmentation error
ram bio wrote: Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Does grompp give any other output, or does it just seg fault? Do other executables work on this system? There are a whole host of issues that could be causing this, from 32/64 bit mismatch, shared libraries being moved, etc, so it is very difficult to diagnose. Was the whole package compiled with MPI (per the above command)? If so, there is no point, since the only MPI-enabled executable is mdrun. It may help to re-compile correctly if this is the case (a bit of a long shot, but perhaps worth trying). Do you have gcc available on the cluster, to test and see if it produces functioning code? -Justin Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul wrote: ram bio wrote: 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) The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs source code download site: "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc." I would suggest updating to the latest version of Gromacs (4.0.7), using a more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and 4.2.x and newer, are fine). 3. Options specified during configuration. I didnot get this, can you please elaborate... Things like --enable-shared, --disable-(whatever), but I don't know that any of this is relevant. I think the compiler is the problem. -Justin 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 (mockbu...@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 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 th
Re: [gmx-users] grompp segmentation error
Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> 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) >> > > The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs > source code download site: > > "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These > compilers come with recent Linux distrubutions like Fedora 5/6 etc." > > I would suggest updating to the latest version of Gromacs (4.0.7), using a > more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and > 4.2.x and newer, are fine). > >> 3. Options specified during configuration. >> >> I didnot get this, can you please elaborate... >> > > Things like --enable-shared, --disable-(whatever), but I don't know that any > of this is relevant. I think the compiler is the problem. > > -Justin > >> >> 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 (mockbu...@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 >> 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 compiler
Re: [gmx-users] grompp segmentation error
ram bio wrote: 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) The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs source code download site: "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc." I would suggest updating to the latest version of Gromacs (4.0.7), using a more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and 4.2.x and newer, are fine). 3. Options specified during configuration. I didnot get this, can you please elaborate... Things like --enable-shared, --disable-(whatever), but I don't know that any of this is relevant. I think the compiler is the problem. -Justin 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 (mockbu...@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 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/m
Re: [gmx-users] grompp segmentation error
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 (mockbu...@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 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 > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp segmentation error
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp segmentation error
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. Thanks, Ram 4 attachments — -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
