AMBER Archive (2006)

Subject: Re: AMBER: fail to execute addles

From: pang zhao (zhao.pang_at_gmail.com)
Date: Tue May 16 2006 - 01:17:05 CDT

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 <zhao.pang_at_gmail.com> 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
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu