Re: [AMBER] Parmed.py deletedihedral

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Tue, 23 Jul 2013 10:37:23 +0000

Hello again,
Thank you for your response.
Here's the output of the printDihedrals command:

> printDihedrals .33
Atom 1 Atom 2 Atom 3 Atom 4 Height Periodic. Phase EEL Scale VDW Scale
33 HG21 (mh) 32 CG2 (fc) 36 CD1 (dc) 37 HD11 (dh) 0.0000 3.0000 0.0000 1.2000 2.0000
33 HG21 (mh) 32 CG2 (fc) 36 CD1 (dc) 38 HD12 (dh) 0.0000 3.0000 0.0000 1.2000 2.0000
33 HG21 (mh) 32 CG2 (fc) 36 CD1 (dc) 39 HD13 (dh) 0.0000 3.0000 0.0000 1.2000 2.0000

(plus a few other dihedrals. The atom types are like that because it is a custom residue.)

Here's output of the deleteDihedral command, executed immediately after the previous one:

> deleteDihedral .33 @32 @36 @37
Deleting dihedral terms involving [.33]-[@32]-[@36]-[@37] (At most 1 total, distinct, dihedrals)
No dihedrals matched -- not deleting any dihedrals

It gives the same result for .33 @32 @36 @38 and @33 @32 @36 @39.It appears to me as if the printDihedral command does identify the dihedral I wish to delete, but I do not understand why the deleteDihedral command does not work.
What am I doing wrong?
Pietro

-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Jason Swails
Sent: 22 July 2013 19:34
To: AMBER Mailing List
Subject: Re: [AMBER] Parmed.py deletedihedral

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 Tue Jul 23 2013 - 04:00:03 PDT
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