Re: [AMBER] Parmed.py deletedihedral

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Tue, 23 Jul 2013 11:43:23 +0000

I have sent the topology file.

-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Jason Swails
Sent: 23 July 2013 12:12
To: AMBER Mailing List
Subject: Re: [AMBER] Parmed.py deletedihedral

On Tue, Jul 23, 2013 at 6:37 AM, Aronica, Pietro < pietro.aronica07.imperial.ac.uk> wrote:

> 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?
>

Can you send me your topology file so I can debug?

Thanks,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 05:00:02 PDT
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