Hello All,
Im trying to create the parameter files of a half cell lithium battery. The molecules involved are Propylene Carbonate, Ethylene Carbonate, PF6-, Graphitic Sheets and Lithium. I previously had problems with the graphite and thanks to you guys I was able to fix it. Now, there seems to be another problem with the Graphic Sheets. I will go through the method to show what I did.
Since the Graphite is the only element I'm having problems with, I will show the .frcmod file for it.
I created the file as follows:
parmchk -i gra_test.mol2 -f mol2 -o frcmod
the resulting file and its contents:
gra_test.frcmod
remark goes here
MASS
BOND
ANGLE
DIHE
ca-ca-cc-cc 1 2.550 180.000 2.000 same as X -c2-ca-X
ca-ca-cc-ha 1 2.550 180.000 2.000 same as X -c2-ca-X
cc-cc-c2-ha 1 6.650 180.000 2.000 same as X -c2-ce-X
ca-cc-c2-ha 1 6.650 180.000 2.000 same as X -c2-ce-X
ca-ca-cc-c2 1 2.550 180.000 2.000 same as X -c2-ca-X
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-ca 1.1 180.0 2.0 Using default value
ca-ca-ca-cc 1.1 180.0 2.0 Using default value
ca-cc-cc-ha 1.1 180.0 2.0 Using default value
c2-ca-cc-cc 1.1 180.0 2.0 Using default value
cc-ha-c2-ha 1.1 180.0 2.0 Using default value
NONBON
I continued on to leap to attempt the generation of the parameter files for the half lithium battery cell as follows.
$AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
-I: Adding /usr/local/amber10/x86_64/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/x86_64/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/x86_64/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/x86_64/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.ff99SB.
Welcome to LEaP!
Sourcing: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber10/x86_64/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/x86_64/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> loadoff PCA.lib
Loading library: ./PCA.lib
> loadoff ECA.lib
Loading library: ./ECA.lib
> loadoff PCB.lib
Loading library: ./PCB.lib
> loadoff GRA.lib
Loading library: ./GRA.lib
> loadoff PF6.lib
Loading library: ./PF6.lib
> min_rep=loadpdb min_rep.pdb
Loading PDB file: ./min_rep.pdb
-- residue 1: duplicate [C138] atoms (total 2)
-- residue 2: duplicate [C138] atoms (total 2)
-- residue 3: duplicate [C138] atoms (total 2)
-- residue 4: duplicate [C138] atoms (total 2)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Added missing heavy atom: .R<GRA 1>.A<C135 195>
Added missing heavy atom: .R<GRA 2>.A<C135 195>
Added missing heavy atom: .R<GRA 3>.A<C135 195>
Added missing heavy atom: .R<GRA 3>.A<C137 163>
Added missing heavy atom: .R<GRA 4>.A<C135 195>
Added missing heavy atom: .R<PCB 5>.A<C4 9>
Added missing heavy atom: .R<PCB 7>.A<C4 9>
Added missing heavy atom: .R<PCB 9>.A<C4 9>
Added missing heavy atom: .R<PCB 11>.A<C4 9>
Added missing heavy atom: .R<PCB 13>.A<C4 9>
Added missing heavy atom: .R<PCB 15>.A<C4 9>
Added missing heavy atom: .R<PCB 17>.A<C4 9>
Added missing heavy atom: .R<PCB 19>.A<C4 9>
Added missing heavy atom: .R<PCB 21>.A<C4 9>
Added missing heavy atom: .R<PCB 23>.A<C4 9>
Added missing heavy atom: .R<PCB 25>.A<C4 9>
Added missing heavy atom: .R<PCB 27>.A<C4 9>
Added missing heavy atom: .R<PCB 69>.A<C4 9>
Added missing heavy atom: .R<PCB 71>.A<C4 9>
Added missing heavy atom: .R<PCB 73>.A<C4 9>
Added missing heavy atom: .R<PCB 75>.A<C4 9>
Added missing heavy atom: .R<PCB 77>.A<C4 9>
Added missing heavy atom: .R<PCB 79>.A<C4 9>
Added missing heavy atom: .R<PCB 81>.A<C4 9>
Added missing heavy atom: .R<PCB 83>.A<C4 9>
Added missing heavy atom: .R<PCB 85>.A<C4 9>
Added missing heavy atom: .R<PCB 87>.A<C4 9>
Added missing heavy atom: .R<PCB 89>.A<C4 9>
Added missing heavy atom: .R<PCB 91>.A<C4 9>
Added missing heavy atom: .R<PCB 159>.A<C4 9>
Added missing heavy atom: .R<PCB 161>.A<C4 9>
Added missing heavy atom: .R<PCB 163>.A<C4 9>
Added missing heavy atom: .R<PCB 165>.A<C4 9>
Added missing heavy atom: .R<PCB 167>.A<C4 9>
Added missing heavy atom: .R<PCB 169>.A<C4 9>
Added missing heavy atom: .R<PCB 171>.A<C4 9>
Added missing heavy atom: .R<PCB 173>.A<C4 9>
Added missing heavy atom: .R<PCB 175>.A<C4 9>
Added missing heavy atom: .R<PCB 177>.A<C4 9>
total atoms in file: 2465
Leap added 175 missing atoms according to residue templates:
39 Heavy
136 H / lone pairs
> saveamberparm min_rep min_rep.prmtop min_rep.inpcrd
Checking Unit.
WARNING: There is a bond of 6.368147 angstroms between:
------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C140 168>
WARNING: There is a bond of 6.355855 angstroms between:
------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C139 166>
WARNING: There is a bond of 8.339007 angstroms between:
------- .R<GRA 1>.A<C137 163> and .R<GRA 1>.A<C138 165>
WARNING: There is a bond of 6.370549 angstroms between:
------- .R<GRA 2>.A<C138 165> and .R<GRA 2>.A<C140 168>
WARNING: There is a bond of 6.357250 angstroms between:
------- .R<GRA 2>.A<C138 165> and .R<GRA 2>.A<C139 166>
WARNING: There is a bond of 8.336572 angstroms between:
------- .R<GRA 2>.A<C137 163> and .R<GRA 2>.A<C138 165>
WARNING: There is a bond of 6.369506 angstroms between:
------- .R<GRA 3>.A<C138 165> and .R<GRA 3>.A<C140 168>
WARNING: There is a bond of 6.359170 angstroms between:
------- .R<GRA 3>.A<C138 165> and .R<GRA 3>.A<C139 166>
WARNING: There is a bond of 9.346460 angstroms between:
------- .R<GRA 3>.A<C137 163> and .R<GRA 3>.A<H6 164>
WARNING: There is a bond of 9.828253 angstroms between:
------- .R<GRA 3>.A<C126 162> and .R<GRA 3>.A<C137 163>
WARNING: There is a bond of 11.735002 angstroms between:
------- .R<GRA 3>.A<C131 97> and .R<GRA 3>.A<H1 98>
WARNING: There is a bond of 9.590395 angstroms between:
------- .R<GRA 3>.A<C131 97> and .R<GRA 3>.A<C132 99>
WARNING: There is a bond of 11.027230 angstroms between:
------- .R<GRA 3>.A<C130 95> and .R<GRA 3>.A<C131 97>
WARNING: There is a bond of 6.372918 angstroms between:
------- .R<GRA 4>.A<C138 165> and .R<GRA 4>.A<C140 168>
WARNING: There is a bond of 6.359739 angstroms between:
------- .R<GRA 4>.A<C138 165> and .R<GRA 4>.A<C139 166>
WARNING: There is a bond of 8.339672 angstroms between:
------- .R<GRA 4>.A<C137 163> and .R<GRA 4>.A<C138 165>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
** No torsion terms for ha-c2-cc-ca
** No torsion terms for ha-c2-cc-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-cc-ca-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-cc-c2-ha
** No torsion terms for ca-cc-c2-ha
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-c2-cc-ca
** No torsion terms for ha-c2-cc-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-cc-ca-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-cc-c2-ha
** No torsion terms for ca-cc-c2-ha
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-c2-cc-ca
** No torsion terms for ha-c2-cc-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-cc-ca-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-cc-c2-ha
** No torsion terms for ca-cc-c2-ha
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-c2-cc-ca
** No torsion terms for ha-c2-cc-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
** No torsion terms for ha-cc-ca-ca
** No torsion terms for c2-cc-ca-ca
** No torsion terms for ca-ca-cc-c2
** No torsion terms for ca-cc-c2-ha
** No torsion terms for ca-cc-c2-ha
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-ca-ca
** No torsion terms for cc-cc-c2-ha
** No torsion terms for cc-cc-c2-ha
** No torsion terms for ca-ca-cc-ha
** No torsion terms for ca-ca-cc-cc
Building improper torsion parameters.
total 282 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
Apparently I have "**No torsion terms for" multiple bonds. I looked and apparently I can manually input these torsion angles but I don't know where to find them after much time of looking. Could someone help me in fixing this issue.
Thanks
Shalton Evans
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Received on Sun Mar 15 2015 - 18:00:04 PDT
