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
