Re: Error running gmx_MMPBSA_test

[Mario Sergio Valdes]

Hi Pedro and welcome!

This error is very strange. I think it is related to bash commands. What OS are you running it on?

El miércoles, 7 de abril de 2021 a las 14:50:27 UTC-5, Pedro escribió:

Hi gmx_MMPBSA users,

I have just installed gmx_MMPBSA and am trying to run the tests to ensure that everything is working fine.  However, when I carry out gmx_MMPBSA_test -f /home/user/Documents -n 10, they all fail and output the following :

GMXMMPBSA.exceptions.MMPBSA_Error: No info files found!. Check the gmx_MMPBSA.log file to report the problem.

Taking the gmx_MMPBSA.log file from the protein_membrane folder as an example, this is the error I get

[INFO   ] Building AMBER Topologies from GROMACS files...

[INFO   ] Checking if supported force fields exists in Amber data...

[INFO   ] Get PDB files from GROMACS structures files...

[INFO   ] Making gmx_MMPBSA index for complex...

[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[ERROR  ] MMPBSA_Error /usr/local/gromacs/bin/gmx editconf failed when querying com.tpr.

GROMACS:      gmx make_ndx, version 2020.3

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:

  gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx

GROMACS reminds you: "Always code as if the person who ends up maintaining your code is a violent psychopath who knows where you live." (Martin Golding)

Going to read 1 old index file(s)

Counted atom numbers up to 46407 in index file

  0 System              : 46407 atoms

  1 Protein             :  2614 atoms

  2 Protein-H           :  1301 atoms

  3 C-alpha             :   163 atoms

  4 Backbone            :   489 atoms

  5 MainChain           :   651 atoms

  6 MainChain+Cb        :   803 atoms

  7 MainChain+H         :   810 atoms

  8 SideChain           :  1804 atoms

  9 SideChain-H         :   650 atoms

 10 Prot-Masses         :  2614 atoms

 11 non-Protein         : 43793 atoms

 12 Other               : 43793 atoms

 13 JZ4                 :    22 atoms

 14 SOD                 :    41 atoms

 15 CLA                 :    47 atoms

 16 TIP3                : 43683 atoms

 nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups

 'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues

 't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help

 'r': residue              'res' nr         'chain' char

 "name": group             'case': case sensitive           'q': save and quit

 'ri': residue index

> 

Syntax error: "-e name 1 GMXMMPBSA_REC"

> 

> 

Copied index group 1 'Protein'

Copied index group 13 'GMXMMPBSA_LIG'

Merged two groups with OR: 2614 22 -> 2636

 17 Protein_GMXMMPBSA_LIG:  2636 atoms

> 

GROMACS:      gmx editconf, version 2020.3

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:

  gmx editconf -f com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx

Reading file com.tpr, VERSION 2018.3 (single precision)

Reading file com.tpr, VERSION 2018.3 (single precision)

Select a group for output:

Group     0 (         System) has 46407 elements

Group     1 (        Protein) has  2614 elements

Group     2 (      Protein-H) has  1301 elements

Group     3 (        C-alpha) has   163 elements

Group     4 (       Backbone) has   489 elements

Group     5 (      MainChain) has   651 elements

Group     6 (   MainChain+Cb) has   803 elements

Group     7 (    MainChain+H) has   810 elements

Group     8 (      SideChain) has  1804 elements

Group     9 (    SideChain-H) has   650 elements

Group    10 (    Prot-Masses) has  2614 elements

Group    11 (    non-Protein) has 43793 elements

Group    12 (          Other) has 43793 elements

Group    13 (  GMXMMPBSA_LIG) has    22 elements

Group    14 (            SOD) has    41 elements

Group    15 (            CLA) has    47 elements

Group    16 (           TIP3) has 43683 elements

Group    17 (Protein_GMXMMPBSA_LIG) has  2636 elements

Select a group: Select a group: Select a group: 

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

Program:     gmx editconf, version 2020.3

Source file: src/gromacs/topology/index.cpp (line 901)

Fatal error:

Cannot read from input

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

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

Note that major changes are planned in future for editconf, to improve usability and utility.

Read 46407 atoms

Volume: 493.039 nm^3, corresponds to roughly 221800 electrons

Velocities found

Error: No such group '-e'

Error: No such group 'GMXMMPBSA_REC_GMXMMPBSA_LIG'

 

Why is editconf unable to read from input? - I have been carrying out MD simulations prior to this and had not had any trouble. 

All help will be greatly appreciated!

Many thanks

Pedro

[Pedro]

Hi Mario,

Thank you for the quick reply and sorry for deleting the first message - it was an accident!

I'm running it on mac OS Catalina version 10.15.7. 

Best regards

Pedro

[Mario Sergio Valdes]

No problem

Unfortunately, we have not tested gmx_MMPBSA on macOS. I will try to test it and make it compatible with macOS

Best!

Mario S.

[Mario Sergio Valdes]

Hi Pedro

After a lot of effort to install macOS, we have done some preliminary tests and it seems to work correctly, however, for some reason in MacOS changing the folder from python generates inconsistencies so gmx_MMPBSA_test does not work correctly for the minimal and all sets. Can you tell us if the manually executed examples work correctly for you?

We will try to find out what happens.

PS: we did the tests in macOS BigSur, it was the only one that we managed to work on. We are not completely familiar with the OS

Best!

Mario S.

[Pedro]

Hi Mario,

Unfortunately manually executed samples do not work for me either. I’ll update by OS to Big Sur and try it there  

Best! 

Pedro

[Pedro]

Hi Mario, 

I’ve upgraded to Mac OS Big Sur. The versions of the software I’m using are ambertools20 which I compiled with gfortran 8.4, python 3.8 and gromacs 2020.3. If you need any other info I'll be happy to provide it. This is the error that I still get: 

[INFO ] Starting
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/xxxx/amber20/bin/cpptraj
[INFO ] tleap found! Using /home/xxxx/amber20/bin/tleap
[INFO ] parmchk2 found! Using /home/xxxx/amber20/bin/parmchk2
[INFO ] sander found! Using /home/xxxx/amber20/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO ] Checking external programs...Done.

[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking if supported force fields exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...

[INFO ] Running command: echo -e name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n | /usr/local/gromacs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx

[INFO ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[INFO ] Running command: echo -e GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx editconf -f com.pdb -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx
[ERROR ] MMPBSA_Error /usr/local/gromacs/bin/gmx editconf failed when querying com.pdb.

Check the gmx_MMPBSA.log file to report the problem.

File "/home/xxxx/amber20/miniconda/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/xxxx/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 97, in gmxmmpbsa
app.make_prmtops()
File "/home/xxxx/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 577, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/xxxx/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 110, in buildTopology
self.gmx2pdb()
File "/home/xxxx/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 167, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(self.editconf), self.FILES.complex_tpr))
File "/home/xxxx/amber20/miniconda/lib/python3.8/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /usr/local/gromacs/bin/gmx editconf failed when querying com.pdb. Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

[Mario Sergio Valdes]

Hi Pedro.

Do you get this error with one of the examples or with your own system?

After upgrading to BigSur did it work correctly?

What version of gmx_MMPSA are you using?

Can you send me the log file gmx_MMPBSA.log?

Best!

Mario S.

[Pedro]

Hi Mario

I get this error with all the examples provided by gmx_MMPBSA_test  

After upgrading to BigSur it still doesn't work

I'm using gmx_MMPBSA version 1.4.0 and I've attached the log file for the protein_membrane example

Best!

Pedro

[Mario Sergio Valdes]

Hello Pedro. Thanks for the info.

Since the error is related to the echo command line, I changed it, so I think it works now. However, I still cannot identify the problem with the execution of gmx_MMPBSA_test. Sympathetically, although it ends in an error, it does show gmx_MMPBSA_ana in the end with the calculations that finished successfully.

Could you test if it now works correctly for you by running the examples individually with gmx_MMPBSA_test or manually?

Best! 

Mario S.

[Mario Sergio Valdes]

Oh, forget it. Update gmx_MMPBSA from Github

[Pedro]

Hello Mario,

After updating gmx_MMPBSA from Github, I ran the tests and all of them except the protein-glycan one passed! It also shows the gmx_MMPBSA_ana with the finished calculations.

Thank you very much, your help was much appreciated!

Pedro 

[Mario Sergio Valdes]

Excellent!

Did you try using the overwrite_data variable in the input file?

Can you tell me about the bug in the Protein-glycan system so I can give full support to gmx_MMPBSA on macOS?

Best!

Mario S.

[Pedro]

Sorry, false alarm! Using the overwrite_data variable in the input file made it work & all tests pass when I re-download the content from the gmx_MMPBSA repository - I must have been using the old files

Thanks again 

Pedro

[Mario Sergio Valdes]

Excellent! We are happy to help you!

Best!

Mario S.