AMBER Archive (2006)

Subject: Re: AMBER: fail to execute addles

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue May 16 2006 - 08:47:37 CDT

you don't need to do minimization or heating if you already equilibrated
before
addles. just go ahead with the dynamics.

pang zhao wrote:
>
> The question is that, should I run constant pressure directly with
> sander.LES or do minimization and then do MD? If I still needs
> minimization, I think I should ask the two questions mentiond above.
>
> All the best
>
> On 5/16/06, *pang zhao* <zhao.pang_at_gmail.com
> <mailto:zhao.pang_at_gmail.com>> wrote:
>
> 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
> <mailto: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
>
>
>
>

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