Thank you for this.
Indeed no warnings are issued by ptraj with the unix line extension \
However, ptraj does not produce any clusters or average structures.
I simply produces 200 individual pdbs from the 1st of the five 2ns trajectories
PTRAJ: trajout test-out representative pdb average pdb averagelinkage clusters 5 mass rms :1-125 .CA prod_2ns.mdcrd.gz: 200 frames.
prod_4ns.mdcrd.gz: 200 frames.
prod_6ns.mdcrd.gz: 200 frames.
prod_8ns.mdcrd.gz: 200 frames.
prod_10ns.mdcrd.gz: 200 frames.
For easy reference I'm adding the latest script:
trajin prod_2ns.mdcrd.gz
trajin prod_4ns.mdcrd.gz
trajin prod_6ns.mdcrd.gz
trajin prod_8ns.mdcrd.gz
trajin prod_10ns.mdcrd.gz
strip :WAT
strip :Na+
trajout test-out representative pdb average pdb averagelinkage \
clusters 5 mass rms :1-125 .CA
On Jun 2, 2011, at 3:36 PM, Thomas Cheatham wrote:
>
>> cluster out test-out representative pdb average pdb averagelinkage
>> clusters 5 mass rms :1-125 .CA
>
> ptraj does not automagically read across line boundaries; you need to
> extend the line as per unix, with \
>
> cluster out test-out representative pdb average pdb averagelinkage \
> clusters 5 mass rms :1-125 .CA
>
> ...otherwise it looks like two cluster commands. The output should have
> shown that it choked on trying to read the second line.
>
> --tom
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 02 2011 - 07:00:03 PDT
