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)
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
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: PF6 number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: PF6 sequence: 1
Created a new atom named: P1 within residue: .R<PF6 1>
Created a new atom named: F1 within residue: .R<PF6 1>
Created a new atom named: F2 within residue: .R<PF6 1>
Created a new atom named: F3 within residue: .R<PF6 1>
Created a new atom named: F4 within residue: .R<PF6 1>
Created a new atom named: F5 within residue: .R<PF6 1>
Created a new atom named: F6 within residue: .R<PF6 1>
Creating new UNIT for residue: PF6 sequence: 2
Created a new atom named: P1 within residue: .R<PF6 2>
Created a new atom named: F1 within residue: .R<PF6 2>
Created a new atom named: F2 within residue: .R<PF6 2>
Created a new atom named: F3 within residue: .R<PF6 2>
Created a new atom named: F4 within residue: .R<PF6 2>
Created a new atom named: F5 within residue: .R<PF6 2>
Created a new atom named: F6 within residue: .R<PF6 2>
total atoms in file: 16
The file contained 14 atoms not in residue templates
> saveamberparm ions ions.prmtop ions.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
FATAL: Atom .R<PF6 1>.A<P1 1> does not have a type.
FATAL: Atom .R<PF6 1>.A<F1 2> does not have a type.
FATAL: Atom .R<PF6 1>.A<F2 3> does not have a type.
FATAL: Atom .R<PF6 1>.A<F3 4> does not have a type.
FATAL: Atom .R<PF6 1>.A<F4 5> does not have a type.
FATAL: Atom .R<PF6 1>.A<F5 6> does not have a type.
FATAL: Atom .R<PF6 1>.A<F6 7> does not have a type.
FATAL: Atom .R<PF6 2>.A<P1 1> does not have a type.
FATAL: Atom .R<PF6 2>.A<F1 2> does not have a type.
FATAL: Atom .R<PF6 2>.A<F2 3> does not have a type.
FATAL: Atom .R<PF6 2>.A<F3 4> does not have a type.
FATAL: Atom .R<PF6 2>.A<F4 5> does not have a type.
FATAL: Atom .R<PF6 2>.A<F5 6> does not have a type.
FATAL: Atom .R<PF6 2>.A<F6 7> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I figured I went through the process correctly but I still failed to produced the .prmtop file. If you or anyone else could help I would greatly appreciate that.
Thanks,
Shalton Evans
________________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Thursday, February 5, 2015 6:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections)
> 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 Fri Feb 13 2015 - 14:00:02 PST
