Hello all,
I am trying to generate a .top file from a single snapshot of a CAMPARI trajectory (.pdb that has gone through pdb4amber) for clustering with cpptraj. However, tleaps' automatic atom reordering results in a top file that no longer matches the trajectory. I want to avoid loading each individual frame (as there are 27,000 frames) into tleap, however I can't find a way to prevent this reordering. I also cannot make use of cpptraj's atommap or parmed's addPDB without a .top that matches the trajectory ordering and CAMPARI doesn't output a topology (only a Z-matrix file in Tinker format). Is there a way to get tleap to adhere to the atom ordering in the pdb, or better yet, a way to reorder the trajectory to match the new top file?
Cheers,
Kari Gaalswyk
Postdoctoral Fellow
University of Denver
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 02 2022 - 11:00:03 PST
