AMBER Archive (2007)

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

From: Lalit Dubey (dubey.lalit_at_gmail.com)
Date: Tue Dec 04 2007 - 18:39:29 CST

Dear All,

Please help me with my question. This could be a very simple question
but as I am new I am stuck at.
I need amber for a very specific purpose of generating
parameter/topology file for novel residues.

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.

Many Thanks,
--- Lalit

Please give a hint for this:

I have a POPS bilayer (128 lipids in total) with 128 Na+ ions and
water above and bottom of the bilayer.

Also, I have generated 'prmtop' and 'inpcrd' files for ONE RESIDUE of
POPS using amber.

Now, I have added water and ions to the bilayer once I built the
bilayer by copying 1 residue of POPS in the space and after generating
the prmtop/inpcrd for 1 residue.
That is, I generated prmtop/inpcrd without solvating the single residue.

Now, to run NAMD, I need parameter file for the whole system (128
lipids+water+ions)! So, how to develop the parameter file for the
whole system from?

Remember, I have prmtop/inpcrd files for 1 POPS residue through amber.
I have parameters for TIP3P water (taken directly from amber ff). I
can have parameters for Na+ as well.
So, in effect I have parameters for 1 POPS residue + 1 Na+ ion + 1
water molecule.

If required I can develop prmtop/inpcrd for 1 POPS and1 Na+ ion
simultaneously but I want to add water only to the bilayer i.e. I
don't want to solvate the 1 residue (of POPS) and generate
prmtop/inpcrd. Also, I have PDB file for the whole system (128
lipids+128 ions+water)

Please give some hint. Also, if required I can come to the lab as per
your availability. Please suggest.

Many Thanks,
--- Lalit
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