Re: [AMBER] Error while running mmpbsa

From: SATYAJIT KHATUA via AMBER <amber.ambermd.org>
Date: Wed, 5 Jul 2023 04:18:28 +0000

Hi,

What is the residue name of Mn. Is it Mn2+?

If yes, provide the mask in your ante-MMPBSA.py script as

ante-MMPBSA-1.py -p com_solvated.prmtop -c com-1.prmtop -s :Na+,Cl-,WAT,K+,Mn2+

ante-MMPBSA-1.py -p com_solvated.prmtop -c ras-1.prmtop -s :Na+,Cl-,WAT,K+,30-60,Mn2+

Hope this helps.

Best,
Satyajit

Get Outlook for Android<https://aka.ms/AAb9ysg>

________________________________
From: Riran via AMBER <amber.ambermd.org>
Sent: Wednesday, July 5, 2023 6:37:43 am
To: amber <amber.ambermd.org>
Subject: [AMBER] Error while running mmpbsa

Hello
I am running mmpbsa in amber18 using the following command "ante-MMPBSA-1.py -p com_solvated.prmtop -c com-1.prmtop -s :Na+,Cl-,WAT,K+
 ante-MMPBSA-1.py -p com_solvated.prmtop -c ras-1.prmtop -s :Na+,Cl-,WAT,K+,30-60
 ante-MMPBSA-1.py -p com_solvated.prmtop -c raf-1.prmtop -s "!(:30-60)" "


And application " MMPBSA-1.py -O -i mmpbsa.in -o mmpbsa.dat -do final_mmpbsa.dat -sp com_solvated.prmtop -cp com-1.prmtop -rp ras-1.prmtop -lp raf-1.prmtop -y md.mdcrd"
But I am encountering an error which says "Beginning GB calculations with /mnt/disk1/software/AMBER18/amber18/bin/sander
  calculating complex contribution...
 bad atom type: Mn
  File "/mnt/disk1/software/AMBER18/amber18/bin/MMPBSA-1.py", line 100, in <module>
    app.run_mmpbsa()
  File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
    self.prmtop))
CalcError: /mnt/disk1/software/AMBER18/amber18/bin/sander failed with prmtop com-1.prmtop!"
But Mn atoms are present in the protein itself.
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 Tue Jul 04 2023 - 21:30:02 PDT
Custom Search