[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

[Alan]

Hi Berk and Mark,


> Erik was too lazy to document this, I now added it to the manual.
>

Is this manual available even via git? When funct 4 and 9 appeared? in gmx
4.5?

Type 4 is identical to type 1, it is only there to distinguish improper from
> proper dihedrals.
>

So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF
generated ligand it would do the same thing, right? I ask that for the grace
of compatibility with gmx 4.0.x.

Type 9 is identical to type 1, except that multiple entries in dihedraltypes
> will lead to
> multiple functions on one dihedral.
>

This one is more difficult to get. I know about multiple entries in CNS,
Charmm and Amber. I was even trying to convert amber99bsc0 new dih
parameters to gromacs and I was using funct 1. However I didn't have Amber
to validate, and now I have Amber11, I don't have time for the moment.

Sounds like funct 9 is to not only pave the way for Charmm, but may help to
address properly the bsc0 parameters, right?

But I need to understand this better. Converting amber's proper dih. param.
to gromacs 4.0.x was done by making these dih. to be RB. However
amb2gmx.plconverts everything to proper (using funct 1) -- acpype is
smarter here. So
in gmx 4.0.x proper dih. funct 1 was never able to interpret multiple
entries on one dihedral?

Now on Mark:


> Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git
> commit a7c597c778351f by Erik, whose message was
>
>    Added support for dihedraltype 9, which allows multiple terms for proper
> dihedrals.
>    By listing a dihedral with type 9, grompp will now scan the force field
> to see if there are
>    multiple terms on _adjacent_ lines listed in the dihedraltypes section,
> and in that case add them all.
>
> A code snippet in src/kernel/toppush.c reads
>
>        if(ft == 9)
>        {
>                /* Previously, we have always overwritten parameters if e.g.
> a torsion
>                 with the same atomtypes occurs on multiple lines. However,
> CHARMM and
>                 some other force fields specify multiple dihedrals over
> some bonds,
>                 including cosines with multiplicity 6 and somethimes even
> higher.
>                 Thus, they cannot be represented with Ryckaert-Bellemans
> terms.
>                 To add support for these force fields, Dihedral type 9 is
> identical to
>                 normal proper dihedrals, but repeated entries are allowed.
>                 */
>                bAllowRepeat = TRUE;
>                ft = 1;
>        }
>

So amb2gmx.pl never worked properly here? For example, I have this for DNA
with amber99bsc0:

; treated as usual propers in GROMACS since Phase angle diff from 0 or 180
degrees
; i   j   k   l func  phase     kd      pn
  2   3   6  23   1   190.98   4.92892   1 ;    O5'-   C5'-   C4'-   C3'
  2   3   6  23   1   295.63   0.38535   2 ;    O5'-   C5'-   C4'-   C3'
  2   3   6  23   1   348.10   4.02848   3 ;    O5'-   C5'-   C4'-   C3'
 28  29  32  33   1    31.80   0.77480   1 ;    O3'-     P-   O5'-   C5'
 28  29  32  33   1   351.96   5.25733   2 ;    O3'-     P-   O5'-   C5'
 28  29  32  33   1   357.25   1.48473   3 ;    O3'-     P-   O5'-   C5'

So, this would only work if funct was 9 and not 1 as above? The way it is,
the last line of a sequence dih. is overwriting the 2 previous one, ignoring
them completely?


> From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it
> can be seen that dihedraltypes 4 and 1 call the same evaluation function.
> Perhaps Erik can confirm this.
>
> src/gmxlib/ifunc.c did suggest to me that something is not quite right...
>
>  def_bonded  ("PDIHS",    "Proper Dih.",     4, 3, 3,  eNR_PROPER, pdihs
>       ),
>  def_bonded  ("RBDIHS",   "Ryckaert-Bell.",  4, 6, 6,  eNR_RB, rbdihs
>      ),
>  def_bonded  ("FOURDIHS", "Fourier Dih.",    4, 4, 4,  eNR_FOURDIH, rbdihs
>       ),
>  def_bonded  ("IDIHS",    "Improper Dih.",   4, 2, 2,  eNR_IMPROPER,idihs
>      ),
>  def_bonded  ("PIDIHS",   "Improper Dih.",   4, 3, 3,  eNR_PROPER, pdihs
>       ),
>
> If PIDIHS is an improper dihedral with the functional form of a proper
> dihedral, should it not use eNR_IMPROPER?
>

I definitely need to run my validations myself, but any words here would be
helpful.

Many thanks you all.

Cheers,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100818/e94ed930/attachment.html>