AMBER Archive (2008)

Subject: AMBER: Querry

From: dipti lele (diptisl86_at_gmail.com)
Date: Wed Aug 13 2008 - 07:15:11 CDT

Hello All,

    I am working with a glycopeptide. And during the simulation the bond
between the threonine and sugar was seen to be broken. I realised that there
was no bond present right from the beginning. I tried to use leap and
command BOND to create a bond. But it gave me following error :
>bond y.11.11 y.20.2
Bond: Maximum coordination exceeded on .R<3VA 20>.A<H1 2>
      -- setting atoms pert=true overrides default limits

What Should I do else to solve the problem.

Thanking you !! 

-- 
Deepti Lele,
NII, New Delhi.

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