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GLYCAM-L  May 2019

GLYCAM-L May 2019

Subject:

Re: [AMBER] tleap error in reading structure generated from GLYCAM web

From:

Lachele Foley <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Tue, 14 May 2019 00:30:16 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (34 lines)

Hi!

You have to issue explicit BOND commands in tleap to connect the
residues back together after adding the TER cards.  If you need help
doing that, just say, but it's pretty easy, and there are good
examples in the tleap docs.

On Mon, May 13, 2019 at 12:30 PM Alejandro Cagnoni
<[log in to unmask]> wrote:
>
> Hi.
>
> How are you? I'm following a thread from a couple of years ago. I've been having problems with branched oligosaccharide structures (generated from glycam web) and tleap (Amber). There is a problem with the conncetions of the atoms.
>
> I've seen that Lachele Foley recommended to add "TER" cards on the pdb file. However, by doing so, even if I've solved the tleap problem, I have problems when minimizing the structure with sander (Amber). The monosaccharides don't remain bound to each other. Could you please help me solve this issue?
>
> Thank you very much.
> Best regards.
>
> --
> Dr. Alejandro J. Cagnoni
>
> Instituto de Biología y Medicina Experimental
> Consejo Nacional de Investigaciones Científicas y Técnicas
> Buenos Aires (1425), Argentina
> (011)47832869. int. 204



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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