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>
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>
>> 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 - 01:00:04 PDT
