Re: [AMBER] 回复: Keyerror about mmpbsa

From: ZangRiran via AMBER <amber.ambermd.org>
Date: Sun, 2 Jul 2023 21:11:55 +0800 (GMT+08:00)

Hi
I set "strip_mask" ,but It still shows the error. Is there any other solution?
Thank you.
Regards.

发件人:Huang ZiJian <Hzj-0820.outlook.com>
发送日期:2023-06-28 11:17:12
收件人:ZangRiran <2115391084.st.gxu.edu.cn>,AMBER Mailing List <amber.ambermd.org>
主题:回复: [AMBER] Keyerror about mmpbsa
Hi,


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


Hope this helps.


Regards,
Zijian

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

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
 Preparing trajectories for simulation...
   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!
 Exiting. All files have been retained."
 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





_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 02 2023 - 06:30:02 PDT
Custom Search