AMBER Archive (2008)

Subject: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits

From: Ted Fischer (
Date: Mon Apr 14 2008 - 07:53:42 CDT

Dear list,

I am experiencing a problem with tleap setting up a system of multiple solutes not connected to another. I am using a pdb file that I manually edited in accordance to the syntax that was previously successful.

I have received an error message like this one after a fixed number of successful steps:

Bond: Maximum coordination exceeded on .R<4SN 1>.A<H62 8>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<4SN 1>.A<H32 9> .R<4SN 1>.A<H62 8>

I have searched for a solution for this problem, tried to find flags that I could set, but there is nothing in the documentation that can help me out.

Hope somebody can point me in the right direction. Thanks in advance...

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