Hi,
Following Bill's comment, if you used ante-MMPBSA.py to create the corresponding topology files, you should define –receptor-mask or –ligand-mask in your command. Check your topology files carefully (i.e., the total number of atoms).
By the way, clarifying your procedure for performing MMPBSA calculation in detail would help find out the cause.
Hope this helps.
P.S.
Giving your feedback in the same message would be fine. Also, it is easy to track your progress.
Regard,
Zijian
________________________________
发件人: ZangRiran via AMBER <amber.ambermd.org>
发送时间: 2023年7月2日 22:01
收件人: Bill Miller III <brmilleriii.gmail.com>; AMBER Mailing List <amber.ambermd.org>
抄送: ZangRiran via AMBER <amber.ambermd.org>
主题: Re: [AMBER] Kerror about MMPBSA
Yes, I used the ante-MMPBSA.py to generate ras.prmtop and raf.prmtop and com.prmtop. It orders is "ante-MMPBSA -p com_solvated.prmtop -c com.prmtop -r ras.prmtop -l raf.prmtop -s :WAT; Cl; K+
发件人：Bill Miller III via AMBER <amber.ambermd.org>
发送日期：2023-07-02 21:31:27
收件人：ZangRiran via AMBER <amber.ambermd.org>
主题：Re: [AMBER] Kerror about MMPBSA>Based on the error, it appears MMPBSA is trying to predict the ligand mask and is finding no atoms. Which is why it is telling you that it “can’t pass no mask to strip” because there are no ligand atoms to remove when preparing the trajectory files. Did you create the dry prmtop files with ante-MMPBSA.py? I would start with double checking that your dry prmtop files were generated correctly.
>
>-Bill
>
>
>
>> On Jul 2, 2023, at 8:22 AM, ZangRiran via AMBER <amber.ambermd.org> wrote:
>>
>> Hello
>> I am running mmpbsa in amber18 using the following command" MMPBSA-1.py -O -i mmpbsa.in -o mmpbsa.dat -do final_mmpbsa.dat -sp com_solvated.prmtop -cp com.prmtop -rp ras.prmtop -lp raf.prmtop -y md.crd"
>> But I am encountering an error which says "Loading and checking parameter files for compatibility...
>> sander found! Using /mnt/disk1/software/AMBER18/amber18/bin/sander
>> cpptraj found! Using /mnt/disk1/software/AMBER18/amber18/bin/cpptraj
>> File "/mnt/disk1/software/AMBER18/amber18/bin/MMPBSA-1.py", line 99, in <module>
>> app.file_setup()
>> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup
>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
>> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 104, in make_trajectories
>> traj.Strip(INPUT['ligand_mask'])
>> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/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!"
>> And the input file MMPBSA content is "
>> &general
>> endframe = 10000,
>> verbose = 1,
>> strip_mask = ":WAT:CL:CLO:IB:K:LI:MG:NA:NB",
>> /
>> &gb
>> igb = 5, saltcon = 0.100,
>> /
>> &pb
>> istrng = 0.100,
>> /
>> &decomp
>> idecomp = 1, print_res = "1-77", dec_verbose = 1,
>> /"
>>
>> How to rectify this kindly help as I am badly stuck in this.
>> Thank you,
>> Regards.
>>
>>
>>
>>
>>
>>
>>
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>
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Received on Sun Jul 02 2023 - 21:30:01 PDT
