Re: [AMBER] Parmed.py deletedihedral

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 22 Jul 2013 14:33:43 -0400

On Mon, Jul 22, 2013 at 12:28 PM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:

> 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?
>

The correct syntax is "deleteDihedral <mask1> <mask2> <mask3> <mask4>" as
you have been using.

There are a couple things to keep in mind here. First, each mask must
select exactly the same number of atoms, and the deleted dihedrals will be
the first atom from each mask followed by the second atom from each mask,
etc.

Second, the dihedral must match 'exactly'. That is, your command will
delete the dihedral between atoms 33--32--36--37. This dihedral will also
match 37--36--32--33, since these two dihedrals are equivalent. Your input
dihedral will not, however, match 33--36--32--37, or any other combination
that is not one of the two I listed above.

Finally, deleteDihedral will delete all dihedrals defined between those
atoms (i.e., if it is a multiterm dihedral, all terms will be removed).

You can use the "printDihedrals" command in ParmEd to make sure that the
dihedral you want to delete exists in the first place.

If the command

printDihedrals .33

does not include 37--36--32--33 or 33--32--36--37, then that dihedral is
not in your topology file. (Perhaps you are numbering from zero, like what
VMD does?)

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jul 22 2013 - 12:00:02 PDT
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