Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom

From: Bill Ross <>
Date: Sun, 08 Dec 2019 18:02:59 -0800

You only have one of (re + lig) in the sum for the two?BillAI:
-------- Original message --------From: venkat <> Date: 12/8/19 5:35 PM (GMT-08:00) To: Subject: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Hello everyone,I tried to run MMPBSA calculation for system, I got error as follows*"**PrmtopError:Complex natom != receptor natom + ligand natom**". *regarding this, I havesearched in the mailing list and I found that, it is related to mismatchedatoms in bound and unbound structure file. So, i examined atoms count in mystructure files with parmed tool and  "summary'  option (parmed_atom-summary.txt<>)total_system.prmtop (1,71,554 atoms), solvent (165885), Na+ (27)complex.prmtop (5,669 atoms)receptor.prmtop (5,643 atoms)ligand.prmtop (26 atoms)And  I checked with notepad also ,(SOL-165858+5669 (re+lig)+27 (Na+) =171554)the command i used is..python2.7 /opt/amber16/bin/ -O -i<> -oFINAL_RESULTS_MMPBSA.dat -sp<> -cpc13.prmtop<> -rpr13.prmtop<> -lpl3.prmtop<>  -yTWO-PARMED.crd<>kindly get the files in attachment<> i don't know where i am mistaking, looking forward to hearing fromyou to rectify the problem.Thank youwith Regardsvenkat_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Sun Dec 08 2019 - 18:30:01 PST
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