Re: [AMBER] Creating a Gold surface library file

From: David A Case <>
Date: Fri, 18 May 2018 07:51:42 -0400

On Thu, May 17, 2018, Timothy Cholko wrote:
> I then placed GLD.lib in $AMBERHOME/dat/leap/lib with all the other .libs.
> I thought that xleap will now read this .lib file and match any
> subsequently loaded pdb file with residue name GLD to this .lib template.

This is not correct. LEaP will search that directory by default, but
you still have to load the libraries you wish to use, e.g. by

  loadOff GLD.lib

before the loadpdb step.

[Explanation: there are, for example, several protein force field
libraries in this directory, each of which defines ALA, VAL, etc. So
LEaP could not just search all the libraries looking for a match: it
needs to be told explicitly which libraries to load.]

...hope this helps....dac

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Received on Fri May 18 2018 - 05:00:02 PDT
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