AMBER Archive (2004)

Subject: AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)

From: Raik Grünberg (
Date: Thu Jul 29 2004 - 05:34:44 CDT


I would like to load a trajectory intro ptraj from which I already stripped
off the hydrogens, removed some residues etc. I.e. what I have is a crd file
and a PDB file of exactly same content. What I DON'T have is a parm file for
the modified PDB/Crd.
Solutions I could think of are:
A) convince tleap to create a parm from the PDB without completing residues
B) create a standard parm with hydrogens but convince ptraj to not expect any
of them

I tried B) with "strip @H*" before trajin but the strip is only executed AFTER
the trajectory is already wrongly read in.

For A) I could do 2 tleap cycles - first creating standard parm / crd files
from the modified PDB, then identifying which atoms have been added by leap
and run tleap again, this time deleting all these atoms with "delete
<unit.resnr.atom_name>". Could that work??
Is there an easier solution?

Many thanks for any advise!
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