[AMBER] mdgx configuration sampling

From: CA gmail <camattelaer01.gmail.com>
Date: Fri, 19 May 2017 13:55:05 +0200

Dear Amber users



I'm using mdgx from AmberTools 17 for configurational sampling of a backbone
in a (modified) dinucleotide molecule. However, apparently mdgx doesn't
recognize atoms, involved in torsions/angles etc., in another residue than
the first. For example, this input file:



-p ../AC.prmtop

-c ../AC.inpcrd

-o GenConformers.out




GridSample :2.P :2.O6' :2.C6' :2.C5'min -180 max 180 Krst 64

maxcyc 10

count 10

verbose 1

outbase 'Conf'

write 'pdb'

outsuff 'pdb'



Gives following statement as output:


Configs >> created 10 initial configurations

Configs >> Processed 0 restraint operations

. (it does complete normally)


And outputs 10 identical configurations. I can additionally add that
removing the ':2' (there is only one possible combination of those 4
atomnames) doesn't help Can this possibly be a bug or is mdgx not meant for
molecules consisting of multiple 'building blocks'? Should I write a new
entry in my prep-file for the dinucleotide or could I alter the .prmtop-file
in a way mdgx would be able to identify the necessary atoms?


Kind regards and thanks in advance


Charles-Alexandre Mattelaer

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Received on Fri May 19 2017 - 05:00:02 PDT
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