Dear AMBER reflector,
I'm writing with a question about the use of tLeap or sLeap for building molecular systems.
I am trying to simulate a set of surface-bound ligands (e.g. linear octane molecules, or molecules with more complicated functionality). To do this, I begin with a MOL2 file with GAFF atomtypes and partial charges for a single ligand, then I creating a (7 ligand)x(7 ligand) supercell using a series of "loadMol2" and "translate" commands in tLeap (bundled with Antechamber 1.27):
> LIG = loadmol2 cand5_lig.mol2
> loadamberparams cand5_lig.frcmod
> ALIG = loadmol2 cand5_lig.mol2
> translate ALIG.1 { -11.25 -11.25 0.0 }
> LIG = combine { LIG ALIG }
> ALIG = loadmol2 cand5_lig.mol2
> translate ALIG.1 { -11.25 -7.50 0.0 }
> LIG = combine { LIG ALIG }
> ALIG = loadmol2 cand5_lig.mol2
> translate ALIG.1 { -11.25 -3.75 0.0 }
> LIG = combine { LIG ALIG }
> ALIG = loadmol2 cand5_lig.mol2
> translate ALIG.1 { -11.25 0 0.0 }
> LIG = combine { LIG ALIG }
> [etc. etc.]
>
> check LIG
> savePdb LIG cand5_lig.pdb
> saveAmberParm LIG cand5_lig.parm7 cand5_lig.inpcrd
I then use the .prmtop file that tLeap creates to carry out a simulation in NAMD, using fixed atoms to represent attachment to a solid surface, although that's not relevant to this question.
So far, so good, but for a second simulation, I would like to simulate the same surface-bound ligands, along with a specific adsorbing molecule, named F2. My current approach is repeat the entire series of commands above, and then do a final "F = loadMol2 F2.mol2" and "combine LIG F." The problem is that the ligands now have their original configuration.
What I would like to do is simply (a) load the cand5_lig.parm7 with 49 ligands, and then (b) load in the PDB coordinates of these 49 ligands' atoms from the final frame of my ligand layer-only simulation. Is there any way to do this with tLeap?
It seems to me that the .prmtop (aka parm7) file would have all the information necessary to recreate the system, and that reassigning coordinates (without changing topology) ought to be pretty simple.
Thanks in advance for any advice that anyone might have!
Best regards,
Nicholas Musolino
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Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino.mit.edu | 617-253-6675 | Room E19-528
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Received on Thu Feb 04 2010 - 13:00:02 PST
