The "Configs >> Processed 0 restraint operations" output means that it
didn't recognize your restraint command. Very likely the apostrophes in
the atom names are the problem--it is thinking that there is a quotation in
there perhaps. First, make sure that there is a space between ":2.C5'
<space> min" and let me have a look at the code for processing keywords
with apostrophes. I know I've programmed it to be able to detect them in
some fashion but I also need to reserve double and single quotations to
demarcate phrases (like ambmasks) that should all be taken as one input.
Try putting additional, double quotations around each of the ambmasks like
this:
GridSample ":2.P" ":2.O6'" ":2.C6'" ":2.C5'" min -180 max 180 Krst 64
I'll have a look in the code to see if there's some other convention you
can use.
Dave
On Fri, May 19, 2017 at 7:55 AM, CA gmail <camattelaer01.gmail.com> wrote:
> 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
>
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>
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Received on Fri May 19 2017 - 09:00:02 PDT
