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
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________________________________
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
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Received on Tue Jul 04 2023 - 21:30:02 PDT
