RE: AMBER: Querry

From: Ross Walker <>
Date: Wed, 13 Aug 2008 07:48:19 -0700

Hi Dipti,


Stop for a minute and read the error message more carefully. Leap is telling
you that the hydrogen atom H1 of residue 20 will have it's maximum
coordination exceeded if it is bonded to atom 11 of residue 11. This seems
to be a perfectly clear and reasonable error message to me. I assume you
don't want a bridging hydrogen atom here. Go back and check that the
residues have the correct protonation states (you may need to build your own
custom ones) and that the atom numbers you are giving to the bond command
are also correct.


Be aware that the next error you are likely to see will be missing
parameters for this bond so if you haven't already you should take a look at
the A1 tutorials on the AMBER site so you know how to create the frcmod file
you will need. You should also check the literature to see what people
typically do for the bond between the sugars and the protein.


Good luck,



From: [] On Behalf Of
dipti lele
Sent: Wednesday, August 13, 2008 5:15 AM
Subject: AMBER: Querry


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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Received on Sun Aug 17 2008 - 06:07:10 PDT
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