On Sun, Sep 19, 2010 at 13:26, case <case.biomaps.rutgers.edu> wrote:
> It's not clear what is in your pdb file; you can use the "setBox" command in
> LEaP to add box info if it is not there. Try out loadPdb and see what you
> get.
My PDB is about as simple as possible. It's just water.
ATOM 1 OW SOL 1 75.670 75.870 35.030 1.00 0.00
ATOM 2 HW1 SOL 1 75.750 75.690 36.010 1.00 0.00
ATOM 3 HW2 SOL 1 74.720 75.780 34.750 1.00 0.00
ATOM 4 OW SOL 2 79.110 75.960 33.670 1.00 0.00
ATOM 5 HW1 SOL 2 78.690 76.830 33.930 1.00 0.00
ATOM 6 HW2 SOL 2 78.430 75.390 33.210 1.00 0.00
[...]
Leap loads the PDB just fine, but it doesn't know the residue SOL, so
I need to set that ahead of time somehow I guess ahead of time?
Unknown residue: SOL number: 1 type: Nonterminal
Unknown residue: SOL number: 2 type: Nonterminal
[...]
Creating new UNIT for residue: SOL sequence: 1
Created a new atom named: OW within residue: .R<SOL 1>
Created a new atom named: HW1 within residue: .R<SOL 1>
Created a new atom named: HW2 within residue: .R<SOL 1>
Creating new UNIT for residue: SOL sequence: 2
Created a new atom named: OW within residue: .R<SOL 2>
Created a new atom named: HW1 within residue: .R<SOL 2>
Created a new atom named: HW2 within residue: .R<SOL 2>
[...]
All I need to do is write out a topology and coordinate file for this
pdb configuration and any water model, which model is basically
insignificant. The simpler the better. Typically in the past when I've
done this for something I was solvating it looked like the following
(using an GAFF forcefield for my solute, ff03 ion, and SPC/E water in
this case). But I don't need any of this for the current case, as I
already have the full configuration built in a single PDB.
source leaprc.ff03.r1
source leaprc.gaff
loadamberparams frcmod.spce
WAT = SPC
LIGAND = loadmol2 stat_input.mol2
addions LIGAND Cl- 1
solvateShell LIGAND SPC 5
saveamberparm LIGAND coords.prmtop coords.inpcrd
Thanks again for your time,
Anthony
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Received on Tue Sep 21 2010 - 09:00:13 PDT
