> On Feb 5, 2015, at 1:22 AM, Evans, Shalton <shalton.ccs.msstate.edu> wrote:
>
> 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
Take note of the names of your atoms: F2, F3, F4, F5, F6, and F7.
> 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
Look at the atom names in your PDB: F1, F2, F3, F4, F5, and F6. The names to not match up, and the off-by-one shift is making tleap line up F2 from the mol2 file with what *should* be F3 from the mol2, and so on down the residue. This is making LEaP very confused.
You either need to fix the PDB file or the mol2 file to ensure that all atom names map correctly between the PDB and mol2 files.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 05 2015 - 04:30:03 PST
