[gmx-users] problem in oplsaa ffbonded.itp

[Mark Abraham]

On 21/03/2012 10:17 PM, francesco oteri wrote:
> OK,
> but for some AMBER dihedral the same goal has been obtained using an X 
> for i and l atoms,
> like:
> X       FE      SS      X       9       0.00    0.0     4
>
> Why the same approach wasn't used for OPLSAA?

Assuming Justin's right, then either approach could have been used. The 
.itp file parsing works by finding which of a large number of scanf 
strings match a given line, so having two ways to do the same thing is 
no big deal. You could argue that not needing to recognise later that X 
means "any atom type" is more efficient, and also that the more terse 
description is less clear to the user. Life == trade-offs :)

Mark

>
>
>
> Il giorno 21 marzo 2012 11:35, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> ha scritto:
>
>
>
>     francesco oteri wrote:
>
>         Dear Gromacs users,
>         I am working on a program that need topology parsing. I am
>         using the OPLSAA forcefield and I noticed that in ffbonded.itp
>         file belonging to this force field there are these strange lines:
>
>         [ dihedraltypes ]
>         ;  i    j    k    l   func     coefficients
>         ; Added DvdS for Quartz simulations
>           SI   OS    1     0.000       3.766      3
>           SI   OH    1     0.000       3.766      3
>
>
>         If it describes dihedral definition, how is possible having
>         only two atom types?
>
>
>     Those are the central two atoms in the dihedral, i.e. atoms j and
>     k in the i-j-k-l notation for a dihedral.
>
>     -Justin
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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>
> -- 
> Cordiali saluti, Dr.Oteri Francesco
>
>

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