AMBER Archive (2007)

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

From: Lalit Dubey (dubey.lalit_at_gmail.com)
Date: Fri Dec 07 2007 - 00:45:59 CST

Hi Dac,

Thanks for the help. Your inputs worked except that I have to source
'leaprc.gaff' instead of 'gaff.dat' and true! there were many pdb
corrections. Also, as and when I have energies from both NAMD and
PMEMD I shall report the group.

Thanks a lot,
--- Lalit

On Dec 4, 2007 7:11 PM, David A. Case <case_at_scripps.edu> wrote:
> 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 leap.in 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 frcmod.xxx (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
> quit
>
>
> 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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