trying to run gmx_MMPBSA on aws

Yoav Atsmon-Raz

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Mar 28, 2022, 4:47:26 AM3/28/22

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Hi everyone,

I've been trying for a while now to setup gmx_MMPBSA to work via batch on AWS and it seems at first to run ok, but then it hangs off when tleap starts preparing its parameters. Specifically at this stage :"[INFO ] Building tleap input files..."

I installed ambertools21 via conda and gmxmmpbsa via pip as instructed in the website.

I'm suspecting that its a permissions issue related to amber but I really don't know how to track them down. Any suggestions will be much appreciated.

All the best, Yoav

marioe911116

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Mar 28, 2022, 5:10:36 AM3/28/22

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Hi there! this is the first time someone reports running gmx_MMPBSA in AWS... could you send around the gmx_MMPBSA.log file to see if we can identify the problem there?

cheers!

Yoav Atsmon-Raz

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Mar 28, 2022, 6:11:27 AM3/28/22

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sure, here you go Mario:

[DEBUG ]

[DEBUG ] Executable: /efs/emendo/users/yoava/gmx-2022-nogpu/bin/gmx

[DEBUG ] Data prefix: /efs/emendo/users/yoava/gmx-2022-nogpu

[DEBUG ] Working dir: /efs/emendo/users/yoava/mmgbsa/ref

[DEBUG ] Command line:

[DEBUG ] gmx editconf -f /efs/emendo/users/yoava/mmgbsa/ref/npt3.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb

[DEBUG ]

[DEBUG ] Select a group for output:

[DEBUG ] Group 0 ( System) has 245642 elements

[DEBUG ] Group 1 ( Protein) has 22622 elements

[DEBUG ] Group 2 ( Protein-H) has 11242 elements

[DEBUG ] Group 3 ( C-alpha) has 1364 elements

[DEBUG ] Group 4 ( Backbone) has 4092 elements

[DEBUG ] Group 5 ( MainChain) has 5457 elements

[DEBUG ] Group 6 ( MainChain+Cb) has 6759 elements

[DEBUG ] Group 7 ( MainChain+H) has 6799 elements

[DEBUG ] Group 8 ( SideChain) has 15823 elements

[DEBUG ] Group 9 ( SideChain-H) has 5785 elements

[DEBUG ] Group 10 ( Prot-Masses) has 22622 elements

[DEBUG ] Group 11 ( non-Protein) has 223020 elements

[DEBUG ] Group 12 ( GMXMMPBSA_LIG) has 3231 elements

[DEBUG ] Group 13 ( NA) has 342 elements

[DEBUG ] Group 14 ( CL) has 226 elements

[DEBUG ] Group 15 ( DNA) has 1577 elements

[DEBUG ] Group 16 ( NA) has 342 elements

[DEBUG ] Group 17 ( CL) has 226 elements

[DEBUG ] Group 18 ( Water) has 217644 elements

[DEBUG ] Group 19 ( SOL) has 217644 elements

[DEBUG ] Group 20 ( non-Water) has 27998 elements

[DEBUG ] Group 21 ( Ion) has 568 elements

[DEBUG ] Group 22 ( NA) has 342 elements

[DEBUG ] Group 23 ( CL) has 226 elements

[DEBUG ] Group 24 ( Water_and_ions) has 218212 elements

[DEBUG ] Group 25 ( GMXMMPBSA_REC) has 24199 elements

[DEBUG ] Group 26 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 27430 elements

[DEBUG ] Select a group:

[DEBUG ] GROMACS reminds you: "You Fill Me With Inertia" (The Long Blondes)

[DEBUG ]

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

[DEBUG ] Read 245642 atoms

[DEBUG ] Volume: 2500.54 nm^3, corresponds to roughly 1125200 electrons

[DEBUG ] No velocities found

[DEBUG ] Selected 12: 'GMXMMPBSA_LIG'

[INFO ] Checking the structures consistency...

[INFO ]

[INFO ] Generating AMBER Compatible PDB Files...

[INFO ] Changing the Complex residues name format from GROMACS to AMBER...

[INFO ] Changing the Receptor residues name format from GROMACS to AMBER...

[INFO ] Changing the Ligand residues name format from GROMACS to AMBER...

[INFO ] Splitting receptor and ligand in PDB files..

[INFO ] Detecting mutation in Receptor. Building Mutant Receptor structure...

[INFO ] Mutating A/5 ILE by ALA

[INFO ] Setting intdiel = intdiel_nonpolar = 1 for Alanine scanning

[INFO ] Mutating A/5 ILE by ALA

[INFO ] Setting intdiel = intdiel_nonpolar = 1 for Alanine scanning

[INFO ] Building tleap input files...

marioe911116

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Mar 28, 2022, 6:17:33 AM3/28/22

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could you please also attach the file called leap.log?

thanks in advance

Yoav Atsmon-Raz

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Mar 28, 2022, 6:18:40 AM3/28/22

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Interestingly, I tried reinstalling the environment via my sys admin and actually got a different error at the same stage.
So based on the output below, I think this might have to do something with how ambertools21 are being linked to gmxmmpbsa

[ERROR ] MMPBSA_Error /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in.

Check the gmx_MMPBSA.log file to report the problem.

File "/efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/bin/gmx_MMPBSA", line 8, in <module>

sys.exit(gmxmmpbsa())

File "/efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa

app.make_prmtops()

File "/efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops

self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

File "/efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 120, in buildTopology

tops = self.makeToptleap()

File "/efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1232, in makeToptleap

GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + 'leap.in'))

File "/efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__

raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')

MMPBSA_Error: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in. Check the gmx_MMPBSA.log file to report the problem.

Yoav Atsmon-Raz

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Mar 28, 2022, 6:23:11 AM3/28/22

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so a bit further digging into the new log files and this is what I saw :

----- Source of /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/cmd/leaprc.protein.ff14SB done

Log file: ./leap.log

Loading parameters: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/parm/parm10.dat

Reading title:

PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA

Loading parameters: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/parm/frcmod.ff14SB

Reading force field modification type file (frcmod)

Reading title:

ff14SB protein backbone and sidechain parameters

Loading library: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/lib/amino12.lib

Loading library: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/lib/aminoct12.lib

Loading library: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/lib/aminont12.lib

Loading library: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/lib/atomic_ions.lib

Loading parameters: /efs/emendo/staging/anaconda3/envs/gmx_MMPBSA/dat/leap/parm/frcmod.ions234lm_126_tip3p

Reading force field modification type file (frcmod)

Reading title:

Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)

Using ArgH and AspGluO modified Bondi2 radii

Loading PDB file: ./_GMXMMPBSA_REC_F1.pdb

total atoms in file: 11242

Leap added 11380 missing atoms according to residue templates:

11380 H / lone pairs

Loading PDB file: ./_GMXMMPBSA_REC_F2.pdb