[AMBER] Lipid 14 format problem

From: Romero, Raquel <raquel.romero.12.ucl.ac.uk>
Date: Mon, 26 Jan 2015 12:44:48 +0000

Dear all,

I want to run MD using amber over a system containing a DPPC lipid bilayer and two proteins. After having my bilayer in Charmm format and converting it into a lipid 14 readable format, I have loaded it in tleap. I have observed that, unlike it is described in the tutorials and references, tleap divides each lipid residue into three and place a TER card after each one of the new residues. (The bibliography says each lipid should remain divided into three residues but all three part of a chain). I think that this format is spoiling my simulations. I have followed the protocol described in papers and tutorials (with the pertinent changes for a DPPC system). My system blows up in the first phase of the 5 ns MD with barostat for equilibrating box dimensions.

Can anyone please tell me what is the way to obtain the right format of Lipid 14 phospholipids? Or how to get forward with my simulation with this apparently wrong format?

Thanks in advance to everyone!

Raquel Romero
PhD Candidate
Department of Pharmaceutical and Biological Chemistry
UCL School of Pharmacy, University College London
29/39 Brunswick Square

T: 0207 753 5972
E: raquel.romero.12.ucl.ac.uk

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Received on Mon Jan 26 2015 - 05:00:03 PST
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