Re: AMBER: querry

From: Lachele Foley (Lists) <"Lachele>
Date: Tue, 22 Jul 2008 09:55:08 -0400


Sorry I missed this posting...

Sandeep is correct (thank you, Sandeep!). It is also important to
make sure that the residues in any pdb files you use follow our naming
conventions. You can learn how we name our residues here:

...and download recent parameters and prep files here:

Or, you might find it useful to build your carbohydrate online:
(see the Biomolecule Builder menu).

You will also find detailed instructions on building oligosaccarides
in the AmberTools manual:

Please write back if you continue to have problems. You can also
contact glycam directly:

:-) Lachele

On Tue, Jul 22, 2008 at 8:09 AM, Sandeep Kaushik
<> wrote:
> 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 Then
> edit your leaprc file to include the new prep file. That should solve your
> problem.
> On 7/14/08, dipti lele <> 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

:-) Lachele
Lachele Foley
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Received on Wed Jul 23 2008 - 06:07:36 PDT
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