[AMBER] Parameterizing cardiolipins in Lipid17 force field

From: Prunotto Alessio <alessio.prunotto.epfl.ch>
Date: Thu, 16 Nov 2017 11:35:52 +0000

Dear Amber community,

I am trying to parameterize cardiolipins within the lipid17 force field. For the polar head, I used a model that is present in literature, and which is working pretty well. However, I am encountering some problems related to the fact that cardiolipins have 4 acyl tails.

First of all, I modified the lipid17.lib library in order to include the cardiolipin head. Then, in the line dedicated to the connectors ( !entry.CDL.unit.connect array int , i.e. the list of 2 atoms to which the acyl tails should be connected), I added two extra-atoms, which are the ones to which the two extra acyl chains should be connected.

In my pdb file, the cardiolipins are structured as follows:

 1) acyl chain

 2) acyl chain

 3) polar head

 4) acyl chain

 5) acyl chain

I used this specific order in order to resemble the - acyl chain, - polar head, - acyl chain order that is required for "ordinary" lipids in the lipid17 force field.

However, when I generate the coordinates and parameters with tleap, I find out that tleap has deleted, for each cardiolipin, 2 acyl chains out of 4, with respect to the original pdb file that I loaded. In particular, it deletes 1) and 4).

I wasn't able to understand which files in the force field I should edit in order to prevent this deletion. Could you help me in this, and/or suggest possible alternatives?

Thank you, and have a good day!

Alessio Prunotto
PhD Student
School of Life Sciences
École Polytechnique Fédérale de Lausanne

Laboratory for Biomolecular Modeling
AAB 015 - Station 19
1015 Lausanne
Phone +41 21 69 31847
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Received on Thu Nov 16 2017 - 04:00:02 PST
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