AMBER Archive (2006)

Subject: Re: AMBER: fail to execute addles

From: pang zhao (zhao.pang_at_gmail.com)
Date: Tue May 16 2006 - 01:39:28 CDT

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> 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> 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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