The xtc center file is not generated

[yajairazepeda]

I have this error in the .err file:

Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_md.tpr, VERSION 2023.2 (single precision)
Reading file VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_md.tpr, VERSION 2023.2 (single precision)
INFO:    Cleaning up image...
/home/b/Yajaira/ASGARD/ASGARD/login_node/input_preparation.sh: line 110: 1986556 Done                    echo 1 0
     1986557 Killed                  | $gmx trjconv -s $RESULTS/molecules/*.tpr -f $RESULTS/molecules/*.xtc -center -ur compact -pbc mol -o "$RESULTS"/molecules/"$NAME"_ori_tmp.xtc
INFO:    Converting SIF file to temporary sandbox...
WARNING: While bind mounting '/home:/home/': destination is already in the mount point list
          :-) GROMACS - gmx trjconv, 2022.5-Ubuntu_2022.5_2ubuntu1 (-:

Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /home/b/Yajaira/ASGARD
Command line:
  gmx trjconv -s VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_md.tpr -f VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_ori_tmp.xtc -fit rot+trans -o VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_center.xtc

-------------------------------------------------------
Program:     gmx trjconv, version 2022.5-Ubuntu_2022.5_2ubuntu1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
    **File 'VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_ori_tmp.xtc'**

[al-rodriguezm]

It appears that the trajectory file generated prior to the centering step (VS_GR_d2_290_ori_tmp.xtc) may not have been created correctly. Could you please show me the previous errors in the .err file?

[yajairazepeda]

These are the previous errors:

Input preparation
singularity exec --bind /home/ /home/b/Yajaira/ASGARD/singularity//ASGARD.simg gmx
Creating analysis folder...
VS_GR_d2_290_results-2023-27-11
mkdir: cannot create directory 'targets/VS_GR_d2_290': File exists
mkdir: cannot create directory 'queries/VS_GR_d2_290': File exists
cp: cannot stat 'd2_290/*.mol2': No such file or directory
Centering trajectory...
INFO:    Converting SIF file to temporary sandbox...
WARNING: While bind mounting '/home:/home/': destination is already in the mount point list
          :-) GROMACS - gmx trjconv, 2022.5-Ubuntu_2022.5_2ubuntu1 (-:

Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /home/b/Yajaira/ASGARD
Command line:
  gmx trjconv -s VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_md.tpr -f VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_md.xtc -center -ur compact -pbc mol -o VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_ori_tmp.xtc

I have a pdb file for the complex (protein-ligand) but I don't know if the mol2 file is necessary. If It is necessary, should I have the mol2 file of the complex or just the ligand?

[suryavasan]

encountering the same issue

[al-rodriguezm]

Could you please attach the generated error log (.err file) so we can know exactly what the problem is? Thank you