On Fri, Feb 13, 2015 at 4:30 PM, Evans, Shalton <shalton.ccs.msstate.edu>
wrote:
> Thanks For your help. I think I did what was suggested but I still could
> not produce the .prmtop file for the PF6-. Could there be any additional
> thing I did wrong? The following is an outline of how I attempted to
> correct the problem.
>
> I changed the pdb file Li_PF6-.pdb ....
>
> REMARK
> ATOM 1 P1 PF6 0 1 3.707 1.738 3.584 1.00 0.00
> ATOM 2 F1 PF6 0 1 2.700 1.368 4.743 1.00 0.00
> ATOM 3 F2 PF6 0 1 2.985 0.720 2.584 1.00 0.00
> ATOM 4 F3 PF6 0 1 4.726 2.144 2.417 1.00 0.00
> ATOM 5 F4 PF6 0 1 4.709 0.590 4.055 1.00 0.00
> ATOM 6 F5 PF6 0 1 4.447 2.772 4.557 1.00 0.00
> ATOM 7 F6 PF6 0 1 2.729 2.894 3.095 1.00 0.00
> TER
> ATOM 8 P1 PF6 0 2 3.707 1.738 23.584 1.00 0.00
> ATOM 9 F1 PF6 0 2 2.700 1.368 24.743 1.00 0.00
> ATOM 10 F2 PF6 0 2 2.985 0.720 22.584 1.00 0.00
> ATOM 11 F3 PF6 0 2 4.726 2.144 22.417 1.00 0.00
> ATOM 12 F4 PF6 0 2 4.709 0.590 24.055 1.00 0.00
> ATOM 13 F5 PF6 0 2 4.447 2.772 24.557 1.00 0.00
> ATOM 14 F6 PF6 0 2 2.729 2.894 23.095 1.00 0.00
> TER
> ATOM 15 Li+ Li+ 3 6.108 9.560 37.381 1.0000 0
> TER
> ATOM 16 Li+ Li+ 4 6.657 19.135 38.538 1.0000 0
> TER
> END
>
> ...to match up with the mol2 file for the PF6-
>
> .<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 F1 0.0000 0.0000 1.6060 f 1 PF6
> -0.408333
> 3 F2 0.0000 1.6060 0.0000 f 1 PF6
> -0.408333
> 4 F3 -1.6060 0.0000 0.0000 f 1 PF6
> -0.408333
> 5 F4 0.0000 0.0000 -1.6060 f 1 PF6
> -0.408333
> 6 F5 0.0000 -1.6060 0.0000 f 1 PF6
> -0.408333
> 7 F6 1.6060 0.0000 0.0000 f 1 PF6
> -0.408333
> .<TRIPOS>BOND
> 1 1 2 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 corrected the shifts and the change the F7 to F6.
>
> I proceeded with the list of commands.
>
> $AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> source leaprc.gaff (to account for lithium ions)
>
This doesn't account for lithium ions. You need to use an ion parameter
file for Lithium.
>
> loadoff PF6-_.lib
> Loading library: ./PF6-_.lib
> > ions = loadpdb Li_PF6-.pdb
> Loading PDB file: ./Li_PF6-.pdb
> Unknown residue: PF6 number: 0 type: Terminal/last
>
This means that the *residue* in the library file does not match the
residue name in the PDB file (PF6). Check your lib file and make sure that
the PF6 residue is actually named PF6. If you use a mol2 file, you need to
use a command like this instead:
PF6 = loadmol2 PF6.mol2
Note you can use the "list" command after you load a library file to check
and see what the residue names were that tleap loaded from the lib file.
Then you just have to make sure they match what's in the PDB.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 13 2015 - 14:00:04 PST
