Re: [gmx-users] pdb2gmx segmentation fault

2011-04-22 Thread Ragothaman Yennamalli
Thanks for the link. Have just filed it. Thanks and Regards, Raghu On Fri, Apr 22, 2011 at 1:12 PM, Justin A. Lemkul wrote: > Matthew Zwier wrote: > >> Nice catch on the readdir_r(). I wonder if the developers would >> appreciate a bug report and patch for your fix. >> >> > Yes, please file an

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-22 Thread Justin A. Lemkul
Matthew Zwier wrote: Nice catch on the readdir_r(). I wonder if the developers would appreciate a bug report and patch for your fix. Yes, please file an issue report on redmine.gromacs.org. If it doesn't get put on a to-do list, it probably won't get done :) -Justin On Fri, Apr 22, 20

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-22 Thread Matthew Zwier
Nice catch on the readdir_r(). I wonder if the developers would appreciate a bug report and patch for your fix. On Fri, Apr 22, 2011 at 1:05 PM, Ragothaman Yennamalli wrote: > Hi all, > With the help of my colleague Nathan Weeks I am able to run pdb2gmx and all > other commands successfully . He

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-22 Thread Ragothaman Yennamalli
Hi all, With the help of my colleague Nathan Weeks I am able to run pdb2gmx and all other commands successfully . Here are his responses which he wanted me to share with you in case someone is trying to install Gromacs in a similar system. We set CFLAGS that way due to the following message when r

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Peter C. Lai
to detect. > Any hints will be appreciated. > > > Please provide the exact commands that you used to install >Gromacs. >What exactly were the issues that you had to circumvent? > Have you > installed previous versions of

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Justin A. Lemkul
Matthew Zwier wrote: Thanks. I'm no Sun expert, so I'd have to echo Justin's request for the precise sequence of commands you used to install GROMACS and all dependencies. In addition, you can add -g to your CFLAGS to get debugging symbols, then execute pdb2gmx via a debugger like gdb. Th

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Matthew Zwier
Thanks. I'm no Sun expert, so I'd have to echo Justin's request for the precise sequence of commands you used to install GROMACS and all dependencies. On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli wrote: > It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. > > On

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli
It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier wrote: > I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused > you to need to define that flag? > > Also...what hardware (cpu) and operating system (linux? w

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Matthew Zwier
I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli
> pdb2gmx, which >> I am not able to detect. >> Any hints will be appreciated. >> >> >> Please provide the exact commands that you used to install >>Gromacs. >>What exactly were the

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Justin A. Lemkul
versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS user

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli
runs perfectly fine. So, there is some issue with pdb2gmx, which >>I am not able to detect. >>Any hints will be appreciated. >> >> >>Please provide the exact commands that you used to install Gromacs. >> What exactly were the issues that you had to c

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Justin A. Lemkul
ave you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users mailto:gmx-users@gro

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli
mands that you used to install Gromacs. What > exactly were the issues that you had to circumvent? Have you installed > previous versions of Gromacs that have worked, such that this problem is > specific to 4.5.4? > > -Justin > > Thanks and Regards, >> Raghu >> >

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Justin A. Lemkul
? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> Message-ID: <4dae452b.3090...@anu.edu.au <mailto:4dae452b.3090...@anu.edu.au>> Content-Type: text/plain; charset=ISO-8859-1

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli
appreciated. Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users Message-ID: <4dae452b.3090...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: > Hi,

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-19 Thread Mark Abraham
On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault witho

[gmx-users] pdb2gmx segmentation fault

2011-04-19 Thread Ragothaman Yennamalli
Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f

Re: [gmx-users] pdb2gmx: segmentation fault

2011-01-13 Thread Kwee Hong
31:35 Subject: Re: [gmx-users] pdb2gmx: segmentation fault Hi Joyce, Can you post the command line? Does it also happen with other force fields? Is there something notable about the pdb file? Cheers, Tsjerk On Jan 13, 2011 7:48 AM, "Kwee Hong" wrote: > > >Hi Mark, > >I

Re: [gmx-users] pdb2gmx: segmentation fault

2011-01-12 Thread Tsjerk Wassenaar
s actually saved as pdb file from autodock output using pymol. Joyce -- *From:* Mark Abraham *To:* Discussion list for GROMACS users *Sent:* Thursday, January 13, 2011 13:43:47 *Subject:* Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong wrote: > >

Re: [gmx-users] pdb2gmx: segmentation fault

2011-01-12 Thread Kwee Hong
Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong wrote: Hi, > > > I was trying to generate topology file of my pdb using pdb2gmx. > > >Select the Force Field: > 0: GROMOS96 43a1 force field > 1: GROMOS96 43a2 force field (improved alkane dihed

Re: [gmx-users] pdb2gmx: segmentation fault

2011-01-12 Thread Mark Abraham
On 01/13/11, Kwee Hong wrote: > > > > > > Hi, > > >  I was trying to generate topology file of my pdb using pdb2gmx. > > > Select the Force Field: >  0: GROMOS96 43a1 force > field  >  1: GROMOS96 43a2 force field (improved alkane dihedrals) >  2: GROMOS96 45a3 force field (Schuler JC

[gmx-users] pdb2gmx: segmentation fault

2011-01-12 Thread Kwee Hong
Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)