Re: [AMBER] 回复: Keyerror about mmpbsa

From: ZangRiran via AMBER <>
Date: Thu, 29 Jun 2023 15:55:46 +0800 (GMT+08:00)

Thank you very much for answering my question.

发件人:Huang ZiJian <>
发送日期:2023-06-28 11:17:12
收件人:ZangRiran <>,AMBER Mailing List <>
主题:回复: [AMBER] Keyerror about mmpbsa

From the error, I guess you need to explicitly define the *strip_mask* on the command line.

Hope this helps.


发件人: ZangRiran via AMBER <>
 发送时间: 2023年6月27日 15:20
 收件人: <>
 主题: [AMBER] Keyerror about mmpbsa

 I am running mmpbsa in amber18 using the following command" -O -i -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
 Preparing trajectories for simulation...
   File "/mnt/disk1/software/AMBER18/amber18/bin/", line 99, in <module>
   File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/", 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/", line 104, in make_trajectories
   File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/", line 646, in Strip
     raise InternalError('Cannot pass no mask to Strip!')
 InternalError: Cannot pass no mask to Strip!
 Exiting. All files have been retained."
 How to rectify this kindly help as I am badly stuck in this.
 Thank you,

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Received on Thu Jun 29 2023 - 01:00:02 PDT
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