[gmx-users] g_mindist error "Cannot open file with NULL filename string"

[ABEL Stephane]

Hello Mark,

Thank you for your response, I have also tested the same command line* with different GMX versions (see below); 

* gmx_mpi mindist -f /ccc/store/cont003/XXX/YYYY/ZZZZ/WWWW/XTC/myXTC.xtc -s MYPDB.pdb -n Hydratation_Protein_OGNG.ndx -b 200000 -e 215000 -dt 4 -d 0.4 -respertime -printresname -group -od 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg -on 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg

With GMX467 ---> OK 


With GMX5.1.4 (segmentation fault) ----------------------

Group     0 (Protein_HeavyAtoms) has  4976 elements
Group     1 (OGNG_AlkylChain) has  1530 elements
Group     2 ( OGNG_Headgroup) has  2244 elements
Group     3 (OGNG_All_HeavyAtoms) has  3774 elements
Group     4 (   Water_oxygen) has 60000 elements
Select a group: Select a group: ^MReading frame       0 time    0.000   ^MReading frame       0 time 200000.000
Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.2#

Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.2#
[irene1022:52095:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
 2 0x0000000000068d1c mxm_handle_error()  /var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:641
 3 0x000000000006926c mxm_error_signal_handler()  /var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:616
 4 0x0000000000035270 killpg()  ??:0
 5 0x00000000000471ad _IO_vfprintf_internal()  :0
 6 0x0000000000051827 __GI_fprintf()  :0
 7 0x00000000003b3cd8 xvgr_header()  ??:0
 8 0x00000000003b3c70 xvgropen_type()  ??:0
 9 0x0000000000545400 dist_plot.a()  gmx_mindist.c:0
10 0x0000000000543990 gmx_mindist()  ??:0
11 0x00000000001e1ff3 _ZN3gmx24Comman

With GMX2018 and 2018.2 (fatal error) ----------------------

Group     0 (Protein_HeavyAtoms) has  4976 elements
Group     1 (OGNG_AlkylChain) has  1530 elements
Group     2 ( OGNG_Headgroup) has  2244 elements
Group     3 (OGNG_All_HeavyAtoms) has  3774 elements
Group     4 (   Water_oxygen) has 60000 elements
Select a group: Select a group: ^MReading frame       0 time    0.000   ^MReading frame       0 time 200000.000
Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.1#

Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.1#

-------------------------------------------------------
Program:     gmx mindist, version 2018
Source file: src/gromacs/fileio/gmxfio.cpp (line 345)

Fatal error:
Cannot open file with NULL filename string

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
+ echo 0 2
+ echo 0 3
+ echo 0 4
+ exit 0

Please note that if I remove the "-group" and "-printresname" arguments the program also crashes, execpt with GMX467.

I will fill a redmine issue

HTH

Stéphane


------------------------------

Message: 5
Date: Tue, 25 Sep 2018 22:23:42 +0200
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] g_mindist error "Cannot open file with NULL
        filename string"
Message-ID:
        <CAMNuMAQR35utSsp8sFP=J20oUd_07Xk-qFLLxMgaUAeRcYKBqw at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

That looks like some kind of bug in mindist. Does an earlier version work
for you? Are you able to upload a report for us at
https://redmine.gromacs.org?

Thanks

Mark

On Tue, Sep 25, 2018 at 3:30 PM ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hi All,
>
> I would like to use g_mindist (vGMX2018.2) to compute the number of total
> contacts between each residue of a protein and surfactant molecules. For
> this I use the following command
>
>  gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n MYNDX.ndx -b 200000 -e
> 215000 -dt 4 -d 0.4 -respertime -printresname -group -od
> Protein_AlkylChain_Contact_min_res.xvg -on
> Protein_AlkylChain_Contact_Number.xvg < Protein_AlkylChain.txt
>
>
>  I obtain the following fatal error, Why ?
>
>  -------------------------------------------------------
> Program:     gmx mindist, version 2018.2
> Source file: src/gromacs/fileio/gmxfio.cpp (line 345)
>
> Fatal error:
> Cannot open file with NULL filename string
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Please note I also would like that each contact between each residue and
> surfactant atoms is counted as one. Is this possible with the command above
> ?
>
> Thanks for you help,
>
> St?phane
>
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