Re: [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////XTC/myXTC.xtc -s 
MYPDB.pdb -n Hydratation_Protein_OGNG.ndx -b 20 -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 6 elements
Select a group: Select a group: ^MReading frame   0 time0.000   
^MReading frame   0 time 20.000
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 0x00068d1c mxm_handle_error()  
/var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:641
 3 0x0006926c mxm_error_signal_handler()  
/var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:616
 4 0x00035270 killpg()  ??:0
 5 0x000471ad _IO_vfprintf_internal()  :0
 6 0x00051827 __GI_fprintf()  :0
 7 0x003b3cd8 xvgr_header()  ??:0
 8 0x003b3c70 xvgropen_type()  ??:0
 9 0x00545400 dist_plot.a()  gmx_mindist.c:0
10 0x00543990 gmx_mindist()  ??:0
11 0x001e1ff3 _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 6 elements
Select a group: Select a group: ^MReading frame   0 time0.000   
^MReading frame   0 time 20.000
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 
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
    
Subject: Re: [gmx-users] g_mindist error "Cannot open file with NULL
filename string"
Message-ID:

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  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 20 -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 al

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

[Mark Abraham]

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  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 20 -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,
>
> Stéphane
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[ABEL Stephane]

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 20 -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,

Stéphane

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.