Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File

From: David A. Case <>
Date: Tue, 4 Dec 2007 17:11:53 -0800

On Tue, Dec 04, 2007, Lalit Dubey wrote:
> I used antechamber/amber9 to generate prmtop/inpcrd file for ONE
> RESIDUE of POPS lipid (without solvating it).
> Then, I replicated one residue in the space to build a lipid bilayer
> (128 lipids in total). Then, I added '128 Na+ ions and water' using a
> simple self code. Thus, I have a PDB file for the whole system that
> includes 128 lipid residues +128 Na+ ion residues + 1018 water
> residues.
> Now, I want to simulate using NAMD.
> My question is: How to generate topology/parameter file for the full
> system that consists 128 POPS lipids + 128 Na+ ions + water?
> Remember, I have amber prmtop for 1 POPS residue, 1 Na+ ion and TIP3.
> I just want a clue for making the prmtop file for the full system.

Should be simple(!??!). Here what the file would look like:

source leaprc.ff94 (to get the water + ions potentials and libraries)
souce gaff.dat (to get the parameters you needed for antechamber)
loadAmberParams (from your antechamber run)
loadAmberPrep POPS.prepi ( " " " " )

x = loadpdb your.pdb.file (having lipids + waters + ions, with TER
                               cards in between separate molecules)
setbox .... (to tell leap about the box parameters that
                               the pdb file was built for).

saveAmberParm x prmtop inpcrd

At the "loadpdb" stage, look at the output carefully, to be sure that all the
atoms in the pdb file are recognized by LEaP. It is quite common that you may
have to edit your pdb file at this point to make LEaP happy.

After this, run with pmemd, which is probably as fast as NAMD except at very
high processor counts. If/when you do switch to NAMD, make sure that it is
giving you the same energies that pmemd is.

[If you used antechamber to build a mol2 file rather than a prepi file, then
replace loadAmberPrep above with loadMol2.]

...hope this helps...dac
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Received on Wed Dec 05 2007 - 06:07:35 PST
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