AMBER Archive (2006)

Subject: Re: AMBER: how to do a molecular dynamic study on a trimer

From: David A. Case (
Date: Sun Aug 13 2006 - 11:37:03 CDT

On Sat, Aug 12, 2006, Gobind Bisht wrote:

> I had a similar problem and i figured out that its
> important that TER is followed with some blank spaces. I mean instead of
> giving newline immediately after typing TER, fill the whole line with blank
> spaces. That worked for me atleast.

This is a semi-bug: TER cards in "real" (RCSB) pdb files have additional
information in them. LEaP currently requires at least one space following
the TER keyword. But this was not something that I knew, and I am tempted
to change this, since having something depend on hard-to-see white space
is not a good interface. (Comments welcome on this.)

Thanks for the report.


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