Really need sleep... This is was supposed to be in answer to the following
email...
-----Original Message-----
From: Yao Yao [mailto:yao0o.ymail.com]
Sent: Wednesday, September 28, 2011 5:29 PM
To: amber.ambermd.org
Subject: [AMBER] 1st DNA tutorial cannot save parameter
Hi,
I am following the very 1st DNA tutorial closely but found I failed to save
the parameters every time I use "saveamberparm".
> -----Original Message-----
> From: Ross Walker [mailto:ross.rosswalker.co.uk]
> Sent: Wednesday, September 28, 2011 9:43 PM
> To: 'AMBER Mailing List'
> Subject: RE: [AMBER] Parameter files :problem to save
>
> Hi Souvik,
>
> The DNA naming convention in PDB files has changed recently and the
> tutorial has been updated to reflect this. Unfortunately that means it
> won't work with AMBER v9. You could try this version of the tutorial
> instead:
>
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: souvik sur [mailto:souviksur.hotmail.com]
> > Sent: Wednesday, September 28, 2011 9:21 PM
> > To: Amber Mailing List
> > Subject: [AMBER] Parameter files :problem to save
> >
> >
> > hello,
> >
> >
> > I am trying to make the initial topology file using ff99bsc0
> forcefield
> > in amber9, the .prepin, .frcmod, .inpcrd, and .prmtop files were
> saved
> > in usual way but when i was trying to add Na+ ions or wanted to
> > solvated by TIP3PBOX 8.0 of my molecule the .prmtop and .inpcrd files
> > were unable to save, I cannot get it. Can you please guide me the
> right
> > path.
> > The error message showed in tleap : parameter file was not saved
> >
> >
> >
> > Please guide me.
> >
> >
> > regards,
> > Souvik Sur
> >
> > Ph. D. Student
> > Department Of Chemistry
> > University Of Delhi
> > India
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Sep 28 2011 - 22:00:06 PDT
