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:
&files
-p ../AC.prmtop
-c ../AC.inpcrd
-o GenConformers.out
&end
&configs
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'
&end
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 19 2017 - 05:00:02 PDT
