Hi,
I think you are missing one keyword input in MMPBSA.py.
There is one keyword input for solvated prmtop. You have to specify that after -sp keyword.
Loke the following:
MMPBSA.py -O -i mmpbsa.in -o mmpbsa.out -sp solv_complex.prmtop -cp dry_complex.prmtop -rp receptor_dry.prmtop -lp ligand_dry.prmtop -y mD.nc
Best,
Satyajit
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________________________________
From: AMANPREET KAUR <akaur_phd21.thapar.edu>
Sent: Monday, June 19, 2023 1:54:58 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Subject: Re: [AMBER] Error while running mmpbsa
Thank you for your guidance.
My dry_complex.prmtop file says
%FLAG POINTERS
%FORMAT(10I8)
4666 16 2340 2378 5359 3214 10591 10090 0 0
25851 289 2378 3214 10090 81 179 198 49 0
0 0 0 0 0 0 0 0 51 0
0
and my receptor_dry.prmtop
%FLAG POINTERS
%FORMAT(10I8)
4615 16 2317 2347 5307 3170 10500 10017 0 0
25559 288 2347 3170 10017 65 152 192 49 0
0 0 0 0 0 0 0 0 24 0
0
and ligand_dry.prmtop
%FLAG POINTERS
%FORMAT(10I8)
51 16 23 31 52 44 91 73 0 0
292 1 31 44 73 16 27 11 49 0
0 0 0 0 0 0 0 0 51 0
0
while running the command it displays an error
MMPBSA.py -O -i mmpbsa.in<
http://mmpbsa.in> -o mmpbsa.out -cp dry_complex.prmtop -rp receptor_dry.prmtop -lp ligand_dry.prmtop -y mD.nc
Loading and checking parameter files for compatibility...
cpptraj found! Using /apps/codes/amber20/amber20_src/bin/cpptraj
mmpbsa_py_energy found! Using /apps/codes/amber20/amber20_src/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
Error: Number of atoms in NetCDF file (51379) does not match number
Error: in associated topology (4666)!
Error: Could not set up 'mD.nc' for reading.
Error: Could not set up input trajectory 'mD.nc'.
Error: Error(s) occurred during execution.
File "/apps/codes/amber20/amber20_src/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py", line 155, in file_setup
self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 66, in make_trajectories
traj = Trajectory(FILES.complex_prmtop, FILES.mdcrd, cpptraj)
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
self.Query()
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 602, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /apps/codes/amber20/amber20_src/bin/cpptraj failed when querying mD.nc
Fatal Error!
Kindly look into it and help me please.
Any other information you let me know
On Mon, Jun 19, 2023 at 1:14 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Hi AMANPREET,
Your input for dry complex looks something like (if your ions are Na+/Cl-, waters have the resname WAT and your ligand is AZM (say))
ante-MMPBSA.py -p solv_8e1x_noh.com.prmtop -c dry_complex.prmtop -s :Na+,Cl-,WAT
ante-MMPBSA.py -p solv_complex.prmtop -c receptor_dry.prmtop -s :Na+,Cl-,WAT,AZM
ante-MMPBSA.py -p solv_complex.prmtop -c ligand_dry.prmtop -s "!(:AZM)"
After generating these, please check if the complex nres = receptor nres + ligand nres.
Best,
Satyajit Khatua
On Mon, Jun 19, 2023 at 1:07 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Hi Amanpreet,
The thing is I have attached a sample input for running the ante-MMPBSA.py. In those inputs you have to replace some lines with appropriate masks.
Like in the following -
ante-MMPBSA.py -p solv_8e1x_noh.com.prmtop -c dry_complex.prmtop -s :ions,water
the ions with the ion(s) you used to neutralize the system (like Na+, Cl- etc.) and the water with a WAT mask. Likewise, for ligand mask you have to use its resname in prmtop i.e. if you have a ligand acetazolamide with resname AZM, then you have to put that as the ligand mask.
----------------------------------------------------------------------------------------------------------------------------------------------------------------
On Mon, Jun 19, 2023 at 12:24 PM AMANPREET KAUR <akaur_phd21.thapar.edu<mailto:akaur_phd21.thapar.edu>> wrote:
Also sir i have used this command to overcome the above error
MMPBSA.py -O -i mmpbsa.in<
http://mmpbsa.in> -o mmpbsa.out -cp dry_complex.prmtop -rp receptor_dry.prmtop -lp ligand_dry.prmtop -y mD.nc
MMPBSA.py -O -i mmpbsa.in<
http://mmpbsa.in> -o mmpbsa.out -cp dry_complex.prmtop -rp receptor_dry.prmtop -lp ligand_dry.prmtop -y mD.nc
Loading and checking parameter files for compatibility...
cpptraj found! Using /apps/codes/amber20/amber20_src/bin/cpptraj
mmpbsa_py_energy found! Using /apps/codes/amber20/amber20_src/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
File "/apps/codes/amber20/amber20_src/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py", line 155, in file_setup
self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 104, in make_trajectories
traj.Strip(INPUT['ligand_mask'])
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 646, in Strip
raise InternalError('Cannot pass no mask to Strip!')
InternalError: Cannot pass no mask to Strip!
Fatal Error!
and hence I got this. What to look for now?
On Mon, Jun 19, 2023 at 12:17 PM AMANPREET KAUR <akaur_phd21.thapar.edu<mailto:akaur_phd21.thapar.edu>> wrote:
Thank you very much for your response. Thanks for sharing the commands and valuable information.
I have used them but unfortunately something went wrong . I am sharing it below:
ante-MMPBSA.py -p solv_8e1x_noh.com.prmtop -c dry_complex.prmtop -s :ions,water
Stripping :ions,water (solvent) from original topology, output is dry_complex.prmtop
Done stripping solvent!
[komol.master 099_-9.5]$ ante-MMPBSA.py -p solv_8e1x_noh.com.prmtop -c receptor_dry.prmtop -s :ions,water,ligand
Stripping :ions,water,ligand (solvent) from original topology, output is receptor_dry.prmtop
Done stripping solvent!
[komol.master 099_-9.5]$ ante-MMPBSA.py -p solv_8e1x_noh.com.prmtop -c ligand_dry.prmtop -s "!(:ligand)"
Stripping !(:ligand) (solvent) from original topology, output is ligand_dry.prmtop
Done stripping solvent!
[komol.master 099_-9.5]$ MMPBSA.py -O -i mmpbsa.in<
http://mmpbsa.in> -o mmpbsa.out -cp dry_complex.prmtop -rp receptor_dry.prmtop -lp ligand_dry.prmtop -y *.nc
Loading and checking parameter files for compatibility...
cpptraj found! Using /apps/codes/amber20/amber20_src/bin/cpptraj
mmpbsa_py_energy found! Using /apps/codes/amber20/amber20_src/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
Error: Number of atoms in NetCDF file (4666) does not match number
Error: in associated topology (51379)!
Error: Could not set up 'nowatermd_8e1x_noh.com2.nc<http://nowatermd_8e1x_noh.com2.nc>' for reading.
Error: Could not set up input trajectory 'nowatermd_8e1x_noh.com2.nc<http://nowatermd_8e1x_noh.com2.nc>'.
Error: Error(s) occurred during execution.
File "/apps/codes/amber20/amber20_src/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py", line 155, in file_setup
self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 66, in make_trajectories
traj = Trajectory(FILES.complex_prmtop, FILES.mdcrd, cpptraj)
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
self.Query()
File "/apps/codes/amber20/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/make_trajs.py", line 602, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /apps/codes/amber20/amber20_src/bin/cpptraj failed when querying nowatermd_8e1x_noh.com2.nc<http://nowatermd_8e1x_noh.com2.nc>
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
How to overcome this. Can you plz share the correct script for running MD. It will help me a lot.
Thank you
On Mon, Jun 19, 2023 at 11:59 AM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Hi Amanpreet,
I am attaching a sample prmtop and pointing you to the residue number. Please check that number in your prmtops.
CHUNK of SAMPLE PRMTOP:
%FORMAT(10I8)
55347 21 53284 2126 4612 2892 9307 8907 0 0
91037 17352 2126 2892 8907 93 209 198 51 1
0 0 0 0 0 0 0 1 24 0
0
%FLAG ATOM_NAME
---------------------------------------------------------------------------------------------------------
The bold one in the prmtop file is the residue number. Please make sure your complex nres = receptor nres + ligand nres
The other way around is that you can use ante-MMPBSA.py to generate the initial prmtop files from the solvated complex prmtop. You can type the command line inputs as follows:
ante-MMPBSA.py -p solv_complex.prmtop -c dry_complex.prmtop -s :ions, water (not the important metal ion(s), if any)
ante-MMPBSA.py -p solv_complex.prmtop -c receptor_dry.prmtop -s :ions,water,ligand
ante-MMPBSA.py -p solv_complex.prmtop -c ligand_dry.prmtop -s "!(:ligand)"
Hope, this may help you to resolve your problem.
Best,
Satyajit
________________________________
From: AMANPREET KAUR <akaur_phd21.thapar.edu<mailto:akaur_phd21.thapar.edu>>
Sent: Monday, June 19, 2023 11:04:14 AM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>>
Subject: Re: [AMBER] Error while running mmpbsa
Thank you sir for your response.
I have not used ante-MMPBSA.py to strip off any atoms or residues.
I have given the topology files which were generated using tleap and antechamber commands for receptor and ligand respectively and mentioned in the script of mmpbsa. But still the error persists.
Can what are the commands to check the no. of residues in a file.
Also plz share the steps or script before running mmpbsa and what to keep in mind to obtain free energy calculations..
On Mon, Jun 19, 2023 at 10:44 AM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Hi Amannpreet,
Your log reads "PrmtopError: Complex nres !=
receptor nres + ligand nres".
Check carefully if your complex residue number equal to receptor residue number + ligand residue number from the respective prmtop file.
If you used ante-MMPBSA.py to extract those check carefully the stripping phase of the complex, receptor and ligand prmtop generation.
Best,
Satyajit
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https://aka.ms/AAb9ysg>
________________________________
From: AMANPREET KAUR via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Sent: Monday, June 19, 2023 10:31:16 AM
To: amber.ambermd.org<mailto:amber.ambermd.org> <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: [AMBER] Error while running mmpbsa
Hlo
I am running mmpbsa in amber 20 using the following command
*MMPBSA.py -O -i mmpbsa.in<
http://mmpbsa.in> <
http://mmpbsa.in/> -o mmpbsa.out
-cp solv_8e1x_noh.com<
http://solv_8e1x_noh.com> <
http://solv_8e1x_noh.com/>.prmtop
-rp 8e1x_noh.prmtop -lp 8480_10.3_opt_chim.prmtop -y *nc*
But I am encountering an error which says "PrmtopError: Complex nres !=
receptor nres + ligand nres.
How to rectify this kindly help as I am badly stuck in this.
Thank you.
Regards
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Received on Mon Jun 19 2023 - 02:00:02 PDT
