Re: AMBER: fail to execute addles

From: pang zhao <>
Date: Tue, 16 May 2006 14:17:05 +0800

Sorry for the seemly stupid two questions.
Because I equilibrate the system first withou LES.
Sorry for the disturbation.

On 5/16/06, pang zhao <> wrote:
> 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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Received on Wed May 17 2006 - 06:07:12 PDT
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