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From: Ross Walker <ross.rosswalker.co.uk>

Date: Wed, 2 Mar 2005 14:37:20 -0800

Dear Yen,

*> As Dr. Junmei has stated I am using
*

*> 0.5 * Vn * (1 + cos(n*phi - gamma))
*

*> Case I
*

*> hc-c3-c -o 1 0.80 0.0 -1. Junmei et al,
*

*> 1999
*

*> hc-c3-c -o 1 0.08 180.0 3. Junmei et al,
*

*> 1999
*

*> Case II
*

*> c3-c3-n-c 1 0.5 180.0 -4. phi,psi,parm94
*

*> c3-c3-n-c 1 0.15 180.0 -3. phi,psi,parm94
*

*> c3-c3-n-c 1 0.53 0.0 1. phi,psi,parm94
*

*> If I encounter such atom types dihedral, should I
*

*> i) consider(ALWAYS) all the 2 sets of parameter (Case
*

*> I) and 3 sets (Case II).
*

Yes you should. So for case one each hc-c3-c-o dihedral term would considt

of the sum of two lots of the equation above. So if X is the dihedral angle

the contribution for each hc-c3-c-o set would be:

0.5*0.8*(1+cos(-x-0.0))+0.5*0.08*(1+cos(3x-180))

And for case 2 each c3-c3-n-c torsion set would be made up of a sum of 3

dihedral terms with the relevant parameters. Let me know if you can manually

match this up. If you find you are slightly off then email me directly and

we can go through an example.

*> ii) since I am doing it manually and there is no
*

*> problem of over counting 1-4 non-bonded interactions.
*

*> Do the sign of the multiplicity(n) affect my
*

*> calculation. What does the -ve multiplicity signify.
*

The -ve multiplicity has no effect of the energy since cos(x)=cos(-x). So

since cos is a symmetric function so the -n makes no difference - hence the

reason it is used as a marker for doing the 1-4NB calculation.

I hope this makes sense.

All the best

Ross

/\

\/

|\oss Walker

| Department of Molecular Biology TPC15 |

| The Scripps Research Institute |

| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |

| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not

be read every day, and should not be used for urgent or sensitive issues.

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Received on Wed Mar 02 2005 - 22:53:00 PST

Date: Wed, 2 Mar 2005 14:37:20 -0800

Dear Yen,

Yes you should. So for case one each hc-c3-c-o dihedral term would considt

of the sum of two lots of the equation above. So if X is the dihedral angle

the contribution for each hc-c3-c-o set would be:

0.5*0.8*(1+cos(-x-0.0))+0.5*0.08*(1+cos(3x-180))

And for case 2 each c3-c3-n-c torsion set would be made up of a sum of 3

dihedral terms with the relevant parameters. Let me know if you can manually

match this up. If you find you are slightly off then email me directly and

we can go through an example.

The -ve multiplicity has no effect of the energy since cos(x)=cos(-x). So

since cos is a symmetric function so the -n makes no difference - hence the

reason it is used as a marker for doing the 1-4NB calculation.

I hope this makes sense.

All the best

Ross

/\

\/

|\oss Walker

| Department of Molecular Biology TPC15 |

| The Scripps Research Institute |

| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |

| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not

be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Mar 02 2005 - 22:53:00 PST

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