[AMBER] peptide and bilayer membrane simulations

From: Chetna Tyagi <cheta231.gmail.com>
Date: Wed, 28 Mar 2018 11:30:27 +0200

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 charmmlipid2amber.py 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

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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