You only have one of (re + lig) in the sum for the two?BillAI:
http://phobrain.com/pr/home/view.html
-------- Original message --------From: venkat <azbvenkat.gmail.com> Date: 12/8/19 5:35 PM (GMT-08:00) To: amber.ambermd.org 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<https://drive.google.com/open?id=1XfseYJqK84O3MnrF7LgXsZdgmNXOuLYb>)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/MMPBSA.py -O -i mmpbsa.in<https://drive.google.com/open?id=1mIlFG7NlAalW2DsMHARuqN9Acp7J2Xn4> -oFINAL_RESULTS_MMPBSA.dat -sp TWO-PARMED.top<https://drive.google.com/open?id=1KO4SMFgvdOfO-njIr-ljaQQJYBHuwiCJ> -cpc13.prmtop<https://drive.google.com/open?id=1kD8KjsMK7Bw5sQvlpiOWvvTCzz5bycZO> -rpr13.prmtop<https://drive.google.com/open?id=1wMJTK3BvTg8fV-kdfowrlPbaZ46hVP4b> -lpl3.prmtop<https://drive.google.com/open?id=1xzk04wCCrN5qAEtGFK6ZX8UONX6cTLgP> -yTWO-PARMED.crd<https://drive.google.com/open?id=1-K5dRiHNCXQ4Fs4uwWdnOASvKi6GSo4y>kindly get the files in attachment<https://drive.google.com/open?id=1RWiStS5RHbTQr2Oc8o8mjRWc9AV7ceqQ>https://drive.google.com/open?id=1RWiStS5RHbTQr2Oc8o8mjRWc9AV7ceqQReally i don't know where i am mistaking, looking forward to hearing fromyou to rectify the problem.Thank youwith Regardsvenkat_______________________________________________AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Dec 08 2019 - 18:30:01 PST
