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.
John
-----Original Message-----
From: Chetna Tyagi [mailto:cheta231.gmail.com]
Sent: Wednesday, March 28, 2018 4:30 AM
To: AMBER Mailing List <amber.ambermd.org>
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 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 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
Chetna
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Received on Wed Mar 28 2018 - 03:00:02 PDT
