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>
> wrote:
>
>> Also sir i have used this command to overcome the above error
>>
>> MMPBSA.py -O -i 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 -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>
>> 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:
>>>
>>> *a*nte-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 -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' for reading.
>>> Error: Could not set up input trajectory '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
>>>
>>> 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> 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>
>>>> *Sent:* Monday, June 19, 2023 11:04:14 AM
>>>> *To:* SATYAJIT KHATUA <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> 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
>>>>
>>>> Get Outlook for Android <https://aka.ms/AAb9ysg>
>>>> ------------------------------
>>>> *From:* AMANPREET KAUR via AMBER <amber.ambermd.org>
>>>> *Sent:* Monday, June 19, 2023 10:31:16 AM
>>>> *To:* amber.ambermd.org <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/> -o mmpbsa.out
>>>> -cp 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
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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Received on Mon Jun 19 2023 - 01:00:03 PDT
