[AMBER] Parmed.py deletedihedral

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Mon, 22 Jul 2013 16:28:28 +0000

Hello,
I was having some trouble with parmed.py, and specifically the deletedihedral command. Based on my, perhaps limited, understanding, this command is used to remove a specific dihedral from a .prmtop file; however, I cannot get it to work. Given four atoms 33, 32, 36 and 37 that form the dihedral in question, I needed to remove this dihedral from the prmtop. Doing it manually ruins the prmtop and doesn't allow pmemd to work with it anymore. I tried with parmed.py, but the I'm unsure of how the syntax is supposed to work.
I have tried

deletedihedral .33 @32 @36 @37
deletedihedral :2.33 :2.32 :2.36 :2.37
deletedihedral :VXI.HG11 :VX1.CG1 :VXI.CD1 :VXI.HD11

but, in all cases, the program says "no dihedrals matched - not deleting any dihedrals".
Did I fundamentally misunderstand what the program is supposed to do? What is the correct syntax?
Kind regards
Pietro
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Received on Mon Jul 22 2013 - 09:30:02 PDT
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