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--- > AMBER General Force Field for organic molecules (Version 1.8, Mar 2015) So I changed to use the gaff.dat from AmberTools15. After that change, the entire diff between leap.log files using AmberTools15 and AmberTools16 is: 1c1 < log started: Tue Jan 31 20:21:26 2017 --- > log started: Tue Jan 31 21:15:45 2017 48c48 < Loading parameters: /home/joao/maindisk/software/amber14/dat/leap/parm/lipid14.dat --- > Loading parameters: /home/joao/maindisk/software/amber16/dat/leap/parm/lipid14.dat 55c55 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/lipid14.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/lipid14.lib 65,67c65,67 < > source leaprc.ff14SB < ----- Source: /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.ff14SB < ----- Source of /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.ff14SB done --- > > source oldff/leaprc.ff14SB > ----- Source: /home/joao/maindisk/software/amber16/dat/leap/cmd/oldff/leaprc.ff14SB > ----- Source of /home/joao/maindisk/software/amber16/dat/leap/cmd/oldff/leaprc.ff14SB done 69c69 < log started: Tue Jan 31 20:21:26 2017 --- > log started: Tue Jan 31 21:15:45 2017 169c169 < Loading parameters: /home/joao/maindisk/software/amber14/dat/leap/parm/parm10.dat --- > Loading parameters: /home/joao/maindisk/software/amber16/dat/leap/parm/parm10.dat 175c175 < Loading parameters: /home/joao/maindisk/software/amber14/dat/leap/parm/frcmod.ff14SB --- > Loading parameters: /home/joao/maindisk/software/amber16/dat/leap/parm/frcmod.ff14SB 183c183 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/amino12.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/amino12.lib 213c213 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/aminoct12.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/aminoct12.lib 241c241 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/aminont12.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/aminont12.lib 267c267 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/nucleic12.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/nucleic12.lib 305c305 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/atomic_ions.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/atomic_ions.lib 374c374 < Loading library: /home/joao/maindisk/software/amber14/dat/leap/lib/solvents.lib --- > Loading library: /home/joao/maindisk/software/amber16/dat/leap/lib/solvents.lib 376a377,380 > Loading: FB3 > Loading: FB3BOX > Loading: FB4 > Loading: FB4BOX 495a500 > >> 498,499c503,504 < ----- Source: /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.gaff < ----- Source of /home/joao/maindisk/software/amber14/dat/leap/cmd/leaprc.gaff done --- > ----- Source: /home/joao/maindisk/software/amber16/dat/leap/cmd/leaprc.gaff > ----- Source of /home/joao/maindisk/software/amber16/dat/leap/cmd/leaprc.gaff done 501c506 < log started: Tue Jan 31 20:21:27 2017 --- > log started: Tue Jan 31 21:15:45 2017 589c594 < Loading parameters: /home/joao/maindisk/software/amber14/dat/leap/parm/gaff.dat --- > Loading parameters: ./gaff.dat 596c601 < Loading parameters: /home/joao/maindisk/software/amber14/dat/leap/parm/frcmod.ionsjc_tip3p --- > Loading parameters: /home/joao/maindisk/software/amber16/dat/leap/parm/frcmod.ionsjc_tip3p If one excludes the differences in the paths, the only difference is in the loading of news solvents (I think? from solvents.lib). These shouldn’t affect. The output .crd is the same, no differences. But the output .prmtop files are different. Namely, - there are differences in the POINTERS section, in the 8th and 15th entry, which correspond to the MPHIA (number of dihedrals not containing hydrogen) and NPHIA (MPHIA + number of constraint dihedrals). The difference is between 7371 and 7373, with AmberTools16 presenting two more: 7,8c7,8 < 7196 17 5555 1670 3625 2269 7454 7371 0 0 < 23114 1552 1670 2269 7371 68 160 213 35 1 --- > 7196 17 5555 1670 3625 2269 7454 7373 0 0 > 23114 1552 1670 2269 7373 68 160 213 35 1 - the previously mentioned entry differences also show in DIHEDRALS_WITHOUT_HYDROGEN: 2097 2106 -2115 2121 44 4383 4392 -4401 4407 44 - lastly, the RADII section, there are multiple differences, where one radius that is 1.2 in AmberTools15, shows as 1.3 in AmberTools16. Sample of differences: 22541,22542c22542,22543 < 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 < 1.30000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00 --- > 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 > 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 The tleap.in file used was this one: # tleap file generated by amber.build source leaprc.lipid14 source leaprc.ff14SB (CHANGED TO oldff/leaprc.ff14SB for AmberTools16) source leaprc.gaff # Loading parameter files loadamberparams frcmod.ionsjc_tip3p # Loading prepi topologies # Loading the system mol = loadpdb input.pdb # Adding disulfide bonds bond mol.22.SG mol.152.SG bond mol.40.SG mol.56.SG bond mol.124.SG mol.225.SG bond mol.131.SG mol.198.SG bond mol.163.SG mol.177.SG bond mol.188.SG mol.212.SG # Writing out the results saveamberparm mol structure.prmtop structure.crd The input.pdb from built from PDB 3PTB. I can share the files that I used and the outputs. Let me know the platform that you prefer for receiving the files. Is there any reason for these differences? We are trying to have a smooth transition from AmberTools15 to AmberTools16 and it would be very helpful to have your insight on these. Thank you. Best regards, João -- _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jan 31 2017 - 13:00:03 PST