Re: [AMBER] peptide and bilayer membrane simulations

From: David A Case <>
Date: Wed, 28 Mar 2018 07:56:07 -0600

On Wed, Mar 28, 2018, Chetna Tyagi wrote:
> 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.

What you should be loading is leaprc.water.tip3p: that has everything
one needs for tip3p water + ions (with parameters compatible with

> 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?

I know this doesn't help much now, but in the upcoming AmberTools18
release (due out in a few weeks) there will be two(!) membrane/bilayer
building programs.


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Received on Wed Mar 28 2018 - 07:00:03 PDT
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