[AMBER] ERROR while using receptor_mask in MMPBSA

From: Amit Sharma \(Asstt. Prof., MCARS\) via AMBER <"Amit>
Date: Tue, 25 Oct 2022 13:35:24 +0530

Hello, I am trying to calculate the binding energy between the specific
residue stretch (from residue :145-267) of the receptor with the ligand.
The whole receptor is of 274 residue. While running the script it gave
following error:
  File "/home/amber20_src/bin/MMPBSA.py", line 98, in <module>
    app.loadcheck_prmtops()
  File "/home/amber20_src/lib/python3.9/site-packages/MMPBSA_mods/main.py",
line 610, in loadcheck_prmtops
    self.normal_system.Map(INPUT['receptor_mask'], INPUT['ligand_mask'])
  File
"/home/amber20_src/lib/python3.9/site-packages/MMPBSA_mods/parm_setup.py",
line 129, in Map
    raise PrmtopError("provided receptor/ligand masks don't select " +
PrmtopError: provided receptor/ligand masks don't select every atom in the
complex topology!
Exiting. All files have been retained.

I am also attaching my input script (mmpbsa.in) :
Input file for running PB and GB
&general
   startframe=1, endframe=59, interval=1,,keep_files=2, use_sander=1,
  entropy=1,verbose=1, receptor_mask=:145-267, ligand_mask=:275-298
/
&gb
  igb=2, saltcon=0.150
/
&pb
  istrng=0.150, radiopt=0,inp=1,
/

I was just wondering what the problem might be? Any suggestions to solve
this error?
Thanks in advance, 
-- 
Sincerely,
*Syeda Amna Arshi*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025
-- 
Sincerely,
*Syeda Amna Arshi*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025
Ph.no: 7737638065
-- 
_
_
*Please consider the environment before printing this email.*
The 
information contained in this electronic message and any *attachments to 
this message are intended for the exclusive use of addressee(s) and may 
contain proprietary, confidential or privileged information. If you are not 
the intended recipient, you should not disseminate, distribute **or copy 
this e-mail. Please notify the
sender immediately and destroy all copies of 
this message and any attachments.***
**
**WARNING***: The recipient should 
check this email and any attachments for
the presence of viruses. JMI 
accepts no liability for any damage caused by any
virus transmitted by this 
email.*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 25 2022 - 01:30:03 PDT
Custom Search