A bit off-track but easy option. CHARMM-GUI has a Glycan Reader which can create a large number of different structures, including substituted polysaccharides. You may find it helpful as it can export files supporting a large number of MD programs including Amber. The only issue is it generates files compatible with CHARMM FF. You may have to convert/reformat files if planning to use another FF.
Regards,
Raman
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________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, April 5, 2020 10:50:28 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cellulose chain
On Thu, Apr 02, 2020, Pinky Mazumder wrote:
>
>I want to build a chain of cellulose. So when I am trying to do this by
>using foo sequence command.
>
> It says that '' Error : sequence : ILLEGAL UNIT named Glc''.
Are you inside tleap at this point? If so, execute the "list" command,
and see if Glc is one of the units listed. If not, you would need to
somehow load the units you want.
Carbohydrates are discussed in Chap. 3 of the Amber Reference Manual:
you might see if that would help.
If this is not a tleap error, then please give more details about
exactly what you mean by "using foo sequence command".
...thx...dac
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Received on Sun Apr 05 2020 - 11:00:02 PDT
