Hi,
I think there is some issue with your extraction using ante-MMPBSA.py. It requires more detail about your system.
In the meantime, you can try the process as following.
The input for extraction looks something like (if your ions are Na+/Cl-, waters have the residue name WAT and your ligand is UNK (say))
ante-MMPBSA.py<
http://ante-mmpbsa.py/> -p solv_8e1x_noh.com.prmtop -c dry_complex.prmtop -s :Na+,Cl-,WAT
ante-MMPBSA.py<
http://ante-mmpbsa.py/> -p solv_complex.prmtop -c receptor_dry.prmtop -s :Na+,Cl-,WAT,UNK
ante-MMPBSA.py<
http://ante-mmpbsa.py/> -p solv_complex.prmtop -c ligand_dry.prmtop -s "!(:UNK)"
Best,
Satyajit
________________________________
From: ZangRiran via AMBER <amber.ambermd.org>
Sent: Monday, July 3, 2023 3:26:27 pm
To: Huang ZiJian <Hzj-0820.outlook.com>; AMBER Mailing List <amber.ambermd.org>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] 回复: Kerror about MMPBSA
HI <br/>I use ante-MMPBSA.py to generate com-1.prmtop , ras-1.prmtop and raf-1.prmtop,but when I run mmpbsa.py it shows "bad atom type" and "CalcError: /mnt/disk1/software/AMBER18/amber18/bin/sander failed with prmtop com-1.prmtop!". I tried "-s ":Mn" "when in antemmpbsa but still.<br/>Do you know how to fix it?<br/>Thank you
发件人：Huang ZiJian via AMBER <amber.ambermd.org>
发送日期：2023-07-03 12:02:25
收件人：AMBER Mailing List <amber.ambermd.org>,ZangRiran <
2115391084.st.gxu.edu.cn>
主题：[AMBER] 回复: Kerror about MMPBSA>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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>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jul 03 2023 - 03:30:03 PDT
