AMBER Archive (2008)

Subject: Re: AMBER: Glycoprotein once again..........

From: Lachele Foley (Lists) (
Date: Thu Aug 14 2008 - 08:28:30 CDT

Do you mind sending the input file(s) and command(s) you used? If
sending the actual files troubles you, can generate a similar set?
You're right that it probably is something smallish. For that reason,
it will be easier for me to find it if I can see exactly what you're

:-) Lachele

On Thu, Aug 14, 2008 at 8:10 AM, dipti lele <> wrote:
> Hello All,
> As per the manual I have tried to build a glycoprotein. I have used
> Glycam online server to generate the glycan aligned to the protein surface.
> I have also changed the names of the residues like thr to OLT etc. Then I
> used the bond command to generate a bond between two atoms as per the
> requirement. It did not show any warning further neither any error. Then I
> made a topology file and parameter file. After the energy minimisation once
> again the bond between the protein and carbohydrate was found to be broken.
> Is there anything else I need to do regarding it. Probably a step in between
> which I have missed. Or some basic mistake which I am doing???
> Thanks a lot
> --
> Deepti Lele,
> NII, New Delhi.

:-) Lachele
Lachele Foley
Athens, GA USA
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