Re: [AMBER] Lipid 14 format problem

From: Romero, Raquel <>
Date: Mon, 26 Jan 2015 16:56:06 +0000

Hi Ross,

Thanks a lot for your reply. This is the output i got:

> pwd

> ./update_amber --show-applied-patches
AmberTools 14 Applied Patches:
update.1, update.2, update.3, update.4, update.5, update.6, update.7, update.8, update.9, update.10,
update.11, update.12, update.13, update.14, update.15, update.16, update.17, update.18, update.19, update.20,
update.21, update.22

Amber 14 Applied Patches:
update.1 (modifies pmemd.amoeba)
update.2 (modifies pmemd)
update.3 (modifies pmemd, pmemd.cuda)
update.4 (modifies pmemd)
update.5 (modifies pmemd)
update.6 (modifies pmemd.cuda, pmemd.cuda.MPI)
update.7 (modifies pmemd, pmemd.MPI)
update.8 (modifies pmemd, pmemd.MPI)

> ls -la $AMBERHOME/bin/*leap*
-rwxr-xr-x 1 root root 10185 Dec 2 12:22 /usr/local/amber14/bin/pytleap
-rwxr-xr-x 1 root root 341 Dec 2 12:20 /usr/local/amber14/bin/tleap
-rwxr-xr-x 1 root root 406 Dec 2 12:20 /usr/local/amber14/bin/xleap

Best wishes

Many thanks


From: Ross Walker <>
Sent: 26 January 2015 15:18
To: AMBER Mailing List
Subject: Re: [AMBER] Lipid 14 format problem

Hi Raquel,

This sounds like a bug in leap that may have been introduced by a recent update - indeed someone in my group reported the same behavior to me earlier this week with our lab copy of AMBER 14 but then switched to our development version and it worked fine so this deserves further investigation. First can you let us know what version of AmberTools and leap you are using. Do the following and copy the output here please:

./update_amber --show-applied-patches
ls -la $AMBERHOME/bin/*leap*


All the best

> On Jan 26, 2015, at 4:44 AM, Romero, Raquel <> wrote:
> 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
> London
> WC1N 1AX
> T: 0207 753 5972
> E:
> _______________________________________________
> AMBER mailing list

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Received on Mon Jan 26 2015 - 09:00:04 PST
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