AMBER Archive (2006)

Subject: Re: AMBER: fail to execute addles

From: pang zhao (zhao.pang_at_gmail.com)
Date: Tue May 16 2006 - 01:13:21 CDT

Dear Prof. DA Case and Prof. Carlos Simmerling

Great thanks for the timely reply!

Now it works when I equilibrate the system without LES first.

During the system up, I neutralize the system with 3 Cl-
and use truncated octahedron periodic box of TIP3P water molecules.
the top and crd files generated by Leap run well and I once useed it for 2ns
NPT MD.

If I use the Leap-generated tom and crd files for LES, the LES generates crd
files
has no periodic system. And it fail to run minimization.

According to the advice of Prof. Carlos, I use the restrt file after 2 ns
NPT MD for LES,
LES generates crd file has periodic system. And I use the LES-generated top
and crd file for minimization, it works!

But I have another two questions for the time.

1. In the amber tutorial, it said that, the system should be heated up to
about 300 K under
constant volume and then switich to constant pressure MD. Is it the same
case for sander.LES?

2. If I use LES to copy the ligand, can I at the same to use position
restraints for the ligand
during minimization or heating process?

Best regards

Pang Zhao

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