Good Day,
I am trying to create a prmtop and coordinate file for a 4 particle mixture of two Li+ ions and 2 PF6- ions. Li+ ions parameters are conveniently in leap but I had to generate mol2 and framed files for PF6-. The mol2 file for PF6- is as follows:
Raptor-login[69] shalton$ vi PF6-_test.mol2
.<TRIPOS>MOLECULE
PF6
7 6 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 P1 0.0000 0.0000 0.0000 p5 1 PF6 1.449998
2 F2 0.0000 0.0000 1.6060 f 1 PF6 -0.408333
3 F3 0.0000 1.6060 0.0000 f 1 PF6 -0.408333
4 F4 -1.6060 0.0000 0.0000 f 1 PF6 -0.408333
5 F5 0.0000 0.0000 -1.6060 f 1 PF6 -0.408333
6 F6 0.0000 -1.6060 0.0000 f 1 PF6 -0.408333
7 F7 1.6060 0.0000 0.0000 f 1 PF6 -0.408333
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
5 1 6 1
6 1 7 1
.<TRIPOS>SUBSTRUCTURE
1 PF6 1 TEMP 0 **** **** 0 ROOT
I then proceeded to create the frcmod file which had no values but i figured this would be ok.
Raptor-login[75] shalton$ parmchk -i PF6-_test.mol2 -f mol2 -o PF6-_test.frcmod
Raptor-login[76] shalton$ vi PF6-_test.frcmod
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON
I then tried to enter this information into leap along with the mixture pdb file of Li+ and PF6- and got could not generate the parameter files for it. I obtained a combination of ERRORS and FATAL ERRORS. This is shown as follows:
Raptor-login[9] shalton$ $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 PF6-.lib
Loading library: ./PF6-.lib
> ion=loadpdb Li_PF6-.pdb
Loading PDB file: ./Li_PF6-.pdb
Created a new atom named: F1 within residue: .R<PF6 1>
ERROR: Comparing atoms
.R<PF6 1>.A<F2 2>,
.R<PF6 1>.A<F3 3>,
.R<PF6 1>.A<F4 4>, and
.R<PF6 1>.A<F5 5>
to atoms
.R<PF6 1>.A<F6 6>,
.R<PF6 1>.A<F5 5>,
.R<PF6 1>.A<F7 7>, and
.R<PF6 1>.A<F2 2>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named F6 from PF6 did not match !
!
!ABORTING.
Where the file "Li_PF6-.pdb can be seen as:
HETATM 1 P1 PF6 0 1 3.707 1.738 3.584 1.00 0.00
HETATM 2 F1 PF6 0 1 2.700 1.368 4.743 1.00 0.00
HETATM 3 F2 PF6 0 1 2.985 0.720 2.584 1.00 0.00
HETATM 4 F3 PF6 0 1 4.726 2.144 2.417 1.00 0.00
HETATM 5 F4 PF6 0 1 4.709 0.590 4.055 1.00 0.00
HETATM 6 F5 PF6 0 1 4.447 2.772 4.557 1.00 0.00
HETATM 7 F6 PF6 0 1 2.729 2.894 3.095 1.00 0.00
TER
HETATM 8 P1 PF6 0 2 3.707 1.738 23.584 1.00 0.00
HETATM 9 F1 PF6 0 2 2.700 1.368 24.743 1.00 0.00
HETATM 10 F2 PF6 0 2 2.985 0.720 22.584 1.00 0.00
HETATM 11 F3 PF6 0 2 4.726 2.144 22.417 1.00 0.00
HETATM 12 F4 PF6 0 2 4.709 0.590 24.055 1.00 0.00
HETATM 13 F5 PF6 0 2 4.447 2.772 24.557 1.00 0.00
HETATM 14 F6 PF6 0 2 2.729 2.894 23.095 1.00 0.00
TER
HETATM 15 Li+ Li+ 3 6.108 9.560 37.381 1.0000 0
TER
HETATM 16 Li+ Li+ 4 6.657 19.135 38.538 1.0000
TER
END
Could I please get some help with this issue. I looked in the archives but the only solution I could find is some 'bug fix 15' for amber8. The problem is I really don't know if that applies to my problem specifically and if it did I have no idea how to apply it as I have a limited background as a programmer. Any helpful advice on how to proceed will be appreciated.
Shalton Evans
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Received on Wed Feb 04 2015 - 22:30:02 PST
