cannot run GBSA calculation on RNA-DNA-Protein complex

Yoav Atsmon-Raz

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Jan 11, 2022, 6:56:17 AM1/11/22

to gmx_MMPBSA

Hey there, I've been trying to run gmx mmpbsa on a trajectory that I ran with amber14sb+OL15 and after preparing a 50 frame trajectory which I removed its PBC I've got the following error:

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

Preparing trajectories for simulation...

Error: # atoms in XTC file (25853) does not match # atoms in parm COM.prmtop (25823)

Error: Could not set up 'COM_traj_0.xtc' for reading.

Error: Could not set up input trajectory 'COM_traj_0.xtc'.

Error: Error(s) occurred during execution.

File "/Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/bin/gmx_MMPBSA", line 8, in <module>

sys.exit(gmxmmpbsa())

File "/Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 97, in gmxmmpbsa

app.file_setup()

File "/Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 145, in file_setup

self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES, self.mpi_size,

File "/Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/lib/python3.8/site-packages/GMXMMPBSA/make_trajs.py", line 68, in make_trajectories

traj = Trajectory(FILES.complex_prmtop, FILES.complex_trajs, cpptraj)

File "/Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/lib/python3.8/site-packages/GMXMMPBSA/make_trajs.py", line 471, in __init__

self.Query()

File "/Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/lib/python3.8/site-packages/GMXMMPBSA/make_trajs.py", line 606, in Query

raise TrajError('%s failed when querying %s' % (self.exe, traj))

TrajError: /Users/yoavatsmonraz/opt/anaconda3/envs/gmxmmpbsa/bin/cpptraj failed when querying COM_traj_0.xtc

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

Can anyone tell me what I'm doing wrong here?

Thanks in advance, Yoav

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marioe911116

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Jan 11, 2022, 12:12:11 PM1/11/22

to gmx_MMPBSA

The fastest way to deal with this kind of error is sending the files so we can work closely with the system and see what's going on... Please, send the files (just send 5 frames of the trajectory) to see if we can solve the problem... Feel free to send me a private message with the files...

Cheers!

Mario E.

Yoav Atsmon-Raz

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Jan 11, 2022, 1:43:47 PM1/11/22

to gmx_MMPBSA

Mario, I'd just like to highlight that they do have different number of atoms as you can see here "...(25853) does not match # atoms in parm COM.prmtop (25823)"

Regardless, attached are my files.

_GMXMMPBSA_MUT_REC.inpcrd.gz

_GMXMMPBSA_MUT_REC_F1.pdb.gz

_GMXMMPBSA_LIG.pdb.gz

_GMXMMPBSA_gb.mdin.gz

_GMXMMPBSA_REC.inpcrd.gz

_GMXMMPBSA_COM.inpcrd.gz

_GMXMMPBSA_LIG.inpcrd.gz

_GMXMMPBSA_MUT_COM.inpcrd.gz

_GMXMMPBSA_REC_F1.pdb.gz

_GMXMMPBSA_LIG_F1.pdb.gz

_GMXMMPBSA_COM.pdb.gz

_GMXMMPBSA_COM_FIXED.pdb.gz

_GMXMMPBSA_REC.pdb.gz

_GMXMMPBSA_leap.in.gz

_GMXMMPBSA_mut_leap.in.gz

_GMXMMPBSA_COM_index.ndx.gz

marioe911116

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Jan 11, 2022, 1:51:08 PM1/11/22

to gmx_MMPBSA

the files I am referring to are the ones you sed for the calculation (*.tpr, *.ndx, *.in, and trajectory files --- just 5 frames)... could you please send those?

cheers!

marioe911116

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Jan 12, 2022, 4:06:05 PM1/12/22

to gmx_MMPBSA

just to sum up as we talked about this issue offline...

the error is due to the presence of a duplicated residue number... this shouldn't happen as it can create conflicts... to solve the problem, it's necessary to create a pdb file out of the *tpr or whichever other file you are using in the "-cs" flag and renumber it... this can be done with editconf in gromacs with the "-resnr 1" flag... using this new renumbered file, everything should run smoothly...

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