AMBER Archive (2008)

Subject: Re: AMBER: querry

From: Sandeep Kaushik (sandy.thesmitten_at_gmail.com)
Date: Tue Jul 22 2008 - 07:09:08 CDT

Hi deepti,
If the version of glycam present on your system doesn't have these UNITS
(especially the N-acetylGal) , download new prep files from glycam.org. Then
edit your leaprc file to include the new prep file. That should solve your
problem.

On 7/14/08, dipti lele <diptisl86_at_gmail.com> wrote:
>
> Hello Sir,
> > I intend to use AMBER for simulating a glycosylated peptide. The
> > structure of it is not known so I need to make a straight chain peptide.
> It
> > has a diasaccharide attached to it. N acetyl galatosamine and galactose.
> How
> > can I make this molecule using tleap. does glycam force filed even
> involve
> > these moieties?
> > Can you please guide me regarding this and what I can do further for
> > getting it?
> >
> > With Regards,
>
> --
> Deepti Lele,
> NII, New Delhi. 

-- 
sandy_thesmitten

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