Re: [AMBER] peptide and bilayer membrane simulations

From: Beale, John <>
Date: Wed, 28 Mar 2018 09:41:50 +0000

Dear AMBER users,

I am having exactly the same issues as Chetna with simulating a peptide and lipid membrane. Any insights and suggestions would be greatly appreciated.


-----Original Message-----
From: Chetna Tyagi []
Sent: Wednesday, March 28, 2018 4:30 AM
To: AMBER Mailing List <>
Subject: [AMBER] peptide and bilayer membrane simulations

Dear all,

As I wrote earlier, I want to simulate a peptide and lipid membrane. The peptide does not need to be inserted. This peptide has engineered residues.

The script does not work even when I chose membrane-only system generated by CHARMM-GUI. The prmtop file is not saved with errors like below.

FATAL: Atom .R<WAT 385>.A<O 1> does not have a type.
Failed to generate parameters.

I see that these errors erupt over only water and K+, Cl- atoms. I always upload the "loadamberparams frcmod.ionsjc_tip3p" and even tried with solvents.lib.

Is there a way to build lipids around or nearby the peptide using only AmberTools? So that I do not have to struggle with conversion?

Please help.

Best wishes
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Received on Wed Mar 28 2018 - 03:00:02 PDT
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