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updated test files
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@stefdoerr
stefdoerr committed May 10, 2024
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Showing 8 changed files with 77 additions and 2,638 deletions.
679 changes: 0 additions & 679 deletions test-amber-build/atomtype-decollisioning/build/structure.prmtop.mod
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This file was deleted.

2 changes: 2 additions & 0 deletions test-amber-build/cyclic-peptide/5VAV/cyclic.pdb
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Original file line number Diff line number Diff line change
Expand Up @@ -201,5 +201,7 @@ ATOM 199 CB ASP A 14 -0.422 2.343 0.801 1.00 32.32 0 C
ATOM 200 CG ASP A 14 -0.447 2.670 -0.679 1.00 32.31 0 C
ATOM 201 OD1 ASP A 14 0.628 2.632 -1.314 1.00 10.15 0 O
ATOM 202 OD2 ASP A 14 -1.542 2.962 -1.203 1.00 51.30 0 O
ATOM 203 HB2 ASP A 14 -1.184 2.930 1.293 1.00 20.03 0 H
ATOM 204 HB3 ASP A 14 0.546 2.614 1.195 1.00 21.54 0 H
ENDMDL
END
70 changes: 35 additions & 35 deletions test-amber-build/cyclic-peptide/5VAV/leap.log
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
log started: Fri May 12 15:31:11 2023
log started: Fri May 10 10:13:38 2024

Log file: ./leap.log
>> #
Expand Down Expand Up @@ -82,19 +82,19 @@ Log file: ./leap.log
>> # Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/parm10.dat
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.ff14SB
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
>> #
>> # Load main chain and terminating amino acid libraries
>> #
>> loadOff amino12.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/amino12.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Expand Down Expand Up @@ -124,7 +124,7 @@ Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/aminoct12.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Expand Down Expand Up @@ -152,7 +152,7 @@ Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/aminont12.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Expand Down Expand Up @@ -223,7 +223,7 @@ Loading: NVAL
>> # Set log file
>> #
>> logFile leap.log
log started: Fri May 12 15:31:11 2023
log started: Fri May 10 10:13:38 2024

Log file: ./leap.log
>> #
Expand Down Expand Up @@ -266,14 +266,14 @@ Log file: ./leap.log
>> # Load the Lipid21 parameter set.
>> #
>> lipid21 = loadamberparams lipid21.dat
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/lipid21.dat
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/lipid21.dat
Reading title:
AMBER Lipid21 v1.0 C. J. Dickson, R.C. Walker, I.R. Gould.
>> #
>> # Load the Lipid21 master lib file.
>> #
>> loadoff lipid21.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/lipid21.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/lipid21.lib
Loading: AR
Loading: CHL
Loading: DHA
Expand All @@ -296,7 +296,7 @@ Loading: ST
----- Source: ./ff2_leaprc.gaff2
----- Source of ./ff2_leaprc.gaff2 done
>> logFile leap.log
log started: Fri May 12 15:31:11 2023
log started: Fri May 10 10:13:38 2024

Log file: ./leap.log
>> #
Expand Down Expand Up @@ -410,15 +410,15 @@ Log file: ./leap.log
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff2.dat
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/gaff2.dat
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
>
> source ff3_leaprc.RNA.Shaw
----- Source: ./ff3_leaprc.RNA.Shaw
----- Source of ./ff3_leaprc.RNA.Shaw done
>> logFile leap.log
log started: Fri May 12 15:31:11 2023
log started: Fri May 10 10:13:38 2024

Log file: ./leap.log
>> # ----- NOTE: this is designed for PDB format 3!
Expand Down Expand Up @@ -504,10 +504,10 @@ Log file: ./leap.log
>> #
>> parm10 = loadamberparams parm10.dat

/home/sdoerr/miniconda3/envs/htmd3.10/bin/teLeap: Note.
/home/sdoerr/miniforge3/envs/htmd/bin/teLeap: Note.
Skipping parm10.dat: already loaded
>> shaw = loadamberparams frcmod.shaw
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.shaw
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.shaw
Reading force field modification type file (frcmod)
Reading title:
# force field modification accoding to Tan et al. Proc. Natl. Acad. Sci. 2018 and N*->NR (purines), NC->ND (Ade(N3,N1)), CB->CE (Ade(C4,C5)), CA->CF (Ade(C6)); and according to Steinbrecher et al. J. Chem. Theory Comput. 2012 and OS->OR (O3' and O5') and O2->OQ (O1P and O2P)
Expand All @@ -516,7 +516,7 @@ Reading title:
>> #
>>
>> loadOff RNA_Shaw.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/RNA_Shaw.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/RNA_Shaw.lib
Loading: A
Loading: A3
Loading: A5
Expand All @@ -535,8 +535,8 @@ Loading: U3
Loading: U5
Loading: UN
>> source leaprc.water.tip4pd
----- Source: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/cmd/leaprc.water.tip4pd
----- Source of /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/cmd/leaprc.water.tip4pd done
----- Source: /home/sdoerr/miniforge3/envs/htmd/dat/leap/cmd/leaprc.water.tip4pd
----- Source of /home/sdoerr/miniforge3/envs/htmd/dat/leap/cmd/leaprc.water.tip4pd done
>>> #
>>> # Load water and ions for TIP4P-ew + Joung-Chetham monovalent ions
>>> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
Expand Down Expand Up @@ -605,7 +605,7 @@ Loading: UN
>>> { "Th4+" "Th" "sp3" }
>>> }
>>> loadOff atomic_ions.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/atomic_ions.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Expand Down Expand Up @@ -674,7 +674,7 @@ Loading: YB2
Loading: ZN
Loading: Zr
>>> loadOff solvents.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/solvents.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Expand Down Expand Up @@ -707,19 +707,19 @@ Loading: TP4
Loading: TP5
Loading: TPF
>>> loadOff tip4pd.off
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/tip4pd.off
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/tip4pd.off
Loading: T4D
Loading: TIP4PDBOX
>>> HOH = T4D
>>> WAT = T4D
>>> loadAmberParams frcmod.tip4pd
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.tip4pd
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.tip4pd
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP4P-D, modified from TIP4PEW.
(UNKNOWN ATOM TYPE: EP)
>>> loadAmberParams frcmod.ions_charmm22
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.ions_charmm22
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.ions_charmm22
Reading force field modification type file (frcmod)
Reading title:
Ion parameters from CHARMM22. Beglov D & Roux B (1994) J. Chem. Phys. 100, 9050-9063.
Expand Down Expand Up @@ -785,7 +785,7 @@ Ion parameters from CHARMM22. Beglov D & Roux B (1994) J. Chem. Phys. 100, 9050-
----- Source: ./ff4_leaprc.DNA.bsc1
----- Source of ./ff4_leaprc.DNA.bsc1 done
>> logFile leap.log
log started: Fri May 12 15:31:12 2023
log started: Fri May 10 10:13:38 2024

Log file: ./leap.log
>> # ----- NOTE: this is designed for PDB format 3!
Expand Down Expand Up @@ -883,7 +883,7 @@ Log file: ./leap.log
>>
>> parm10 = loadamberparams parm10.dat

/home/sdoerr/miniconda3/envs/htmd3.10/bin/teLeap: Note.
/home/sdoerr/miniforge3/envs/htmd/bin/teLeap: Note.
Skipping parm10.dat: already loaded
>>
>> #
Expand Down Expand Up @@ -978,7 +978,7 @@ Substituting map O2P -> OP2 for O2P -> OP2
>> }
>>
>> loadoff parmBSC1.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/parmBSC1.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/parmBSC1.lib
Loading: DA
Loading: DA3
Loading: DA5
Expand All @@ -996,7 +996,7 @@ Loading: DT3
Loading: DT5
Loading: DTN
>> loadamberparams frcmod.parmbsc1
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.parmbsc1
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.parmbsc1
Reading force field modification type file (frcmod)
Reading title:
Parmbsc1 force-field for DNA
Expand Down Expand Up @@ -1081,7 +1081,7 @@ Parmbsc1 force-field for DNA
>> { "Th4+" "Th" "sp3" }
>> }
>> loadOff atomic_ions.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/atomic_ions.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Expand Down Expand Up @@ -1150,7 +1150,7 @@ Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/lib/solvents.lib
Loading library: /home/sdoerr/miniforge3/envs/htmd/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Expand Down Expand Up @@ -1185,22 +1185,22 @@ Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> loadAmberParams frcmod.tip3p
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.tip3p
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
>> loadAmberParams frcmod.ions1lm_126_tip3p
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.ions1lm_126_tip3p
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
>> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.ionsjc_tip3p
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
>> loadAmberParams frcmod.ions234lm_126_tip3p
Loading parameters: /home/sdoerr/miniconda3/envs/htmd3.10/dat/leap/parm/frcmod.ions234lm_126_tip3p
Loading parameters: /home/sdoerr/miniforge3/envs/htmd/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Expand All @@ -1218,9 +1218,9 @@ Clearing name map.
> cyc = loadpdb cyclic.pdb
Loading PDB file: ./cyclic.pdb
Matching PDB residue names to LEaP variables.
total atoms in file: 202
Leap added 7 missing atoms according to residue templates:
7 H / lone pairs
total atoms in file: 204
Leap added 5 missing atoms according to residue templates:
5 H / lone pairs
> bond cyc.1.N cyc.14.C
> mol = combine {mol cyc}
combine: mol is type String
Expand Down
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