Dear Amber Users,
I have two different simulations for one protein, one start from folding
structure another one from unfolded and the have two different topologies
and coordinate file. I want to calculate the native contacts for my
simulation and use the first snapshot of the folded simulation as the
reference file. It is easy for folded, but I do not know how to do that for
unfolded. In this case is there any way for using the first snapshot of my
folded structure for the unfolded case?
In general, I want to know, is there any way to use topology or coordinate
or restart file of one simulation as an input file for another simulation?
this my input file ( I tried to strip water and ions from my trajectory and
use the PDB file(which I strip water and ions from it too) as the reference
but it did not work).
parm 1WJB-OPC-FF10-UHm.top
trajin 1WJB-OPC-FF10-UHm.prod1.traj
reference ref-folded.pdb
strip :WAT
strip :Na+
strip :Cl-
nativecontacts :1-55&!.H= writecontacts contacts.dat out numcontacts.dat
reference ref-folded.pdb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 17 2016 - 09:30:04 PDT
