**From:** Jrme Hnin (*jhenin_at_ifr88.cnrs-mrs.fr*)

**Date:** Fri Jul 02 2010 - 07:13:10 CDT

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Hi,

Before you do what you are planning, are you sure the dihedral energy

term is the information you want? The complete torsional potential

results from the "dihedral" terms, added to 1-4 LJ and Coulomb, and

some amount of additional (1-5 and further away) non-bonded

interactions.

Jerome

On 1 July 2010 12:07, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> wrote:

*> Hello,
*

*> This might be more of a CHARMM force-field question, but since I'm more
*

*> comfortable in the NAMD community I'll try here first :)
*

*> In the CHARMM force-field there are dihedral angle potential functions for
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*> quadruples of atoms.
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*> So, if I'd like to plot the potential function for a rotation around a bond,
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*> then should I sum the potential functions for all possible quadruples around
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*> that bond?
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*> For example if I wanted to plot the potential for the rotation around the
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*> first bond in 2-chloropropanol then should I sum the following terms:
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*>
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*> HO Cl
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*> \ /
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*> H -- C -- C -- CH3
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*> / \
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*> H H
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*>
*

*> O - C - C - Cl
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*> O - C - C - C
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*> O - C - C - H
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*> H - C - C - Cl x 2 (each with different offset?)
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*> H - C - C - C x 2
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*> H - C - C - H x 2
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*> and in propan just
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*> H H
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*> \ /
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*> H -- C -- C -- CH3
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*> / \
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*> H H
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*> H - C - C - H x 6 (each with diffrent offset?)
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*> H - C - C - H x 3
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*> Any suggestions about what would be the easiest way to obtain the potential
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*> for rotation around each single bond for every amino acid side-chain?
*

*> I'm thinking of either parsing the topology file directly, getting all
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*> combinations of dihedrals and looking this up in the parameter file (a bit
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*> complicated).
*

*> Or perhaps I could generate a peptide composed of all the difrent amino
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*> acids, then I have the dehidrals in the psf files, so I just look up all the
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*> combinations in the parameter file (still complicated but not that much).
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*> Perhaps I'm missing something and this is trivial to do in another way?
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*>
*

*> thank you for your help & best regards,
*

*> Ajasja
*

**Next message:**Ajasja Ljubetič: "Re: Dihedral angle potential energy function"**Previous message:**David Kelly: "Help: NAMD on cluster; nodes reject multiple connections"**In reply to:**Ajasja Ljubetič: "Dihedral angle potential energy function"**Next in thread:**Ajasja Ljubetič: "Re: Dihedral angle potential energy function"**Reply:**Ajasja Ljubetič: "Re: Dihedral angle potential energy function"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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