AMBER Archive (2006)

Subject: Re: AMBER: xleap problem

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Jun 06 2006 - 18:42:34 CDT

If you don't have any problem of your system.
Why do you want to save prep file?
You can run the simulation.

Usually, when I introduce new residue or organic molecule ,
I use antechamber to produce prep file, to let the leap
recognize the new molecule.

If your goal is not running MD,
I don't know why the manual doesn't have information for "saveamberprep".

On 6/6/06, Myunggi Yi <myunggi_at_gmail.com> wrote:
> There is no saveAmberPrep in "leap" command from the manual.
> You may want to read "Antechamber" manual.
>
>
> On 6/6/06, Hashem Taha <hashemt_at_gmail.com> wrote:
> > i am trying to make prep file (from my pdb file) using xleap, but every time
> > i try to use 'saveAmberPrep unit file.prep' xleap says that it's saving the
> > prep file (saving prep, residue unit ...), but it just freezes at that point
> > and crashes. I have tried doing this on several computers, all of which gave
> > the same result. there were no errors in the unit after using 'check unit'
> > and all the connect points were set properly. There were also no error
> > messages given. I don't what is going on. any help is appreciated. the pdb
> > file of the molecule i am using is attached if needed.
> >
> >
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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