[gmx-users] Re: phosphotyrosine

David van der Spoel spoel at xray.bmc.uu.se
Sat Apr 27 10:59:36 CEST 2002

On Fri, 26 Apr 2002, Graham Smith wrote:

>[ SEP ]
> [ dihedrals ]
>   CB    OG     P   O1P     gd_9
>   CB    OG     P   O1P     gd_11
>is this correct? One of these has multiplicity 2, one 3. 
>So it would make sense if there's double bond character I guess. 
What you are doing here is adding two cosines to give you a slightly more
complicated function with the minimum at 180 and two less deep minima
close to 60 and -60 (but not exactly there). This potential is added to
the 1-4 interaction and together they should describe the rotation around
the OG-P bond. The 1-4 will make the 180 minimum even deeper with respect
to the other two. I can't judge whether this is correct, you would have to
do quantum calculations of the angle dependence of the energy.

>To use Hansson, Nordlund and Aqvist's parameters I had to introduce a new
>atom type OP. I let gromacs use the normal Cij = sqrt(Cii Cjj) combination
>rules for normal LJ, which was what Hansson et al did, but I seemed to
>need explicit combination rules for LJ-14 if I was not to get zeros, so I
>just used the same ones as for OA. Seem OK?
This seems incorrect. The 1-4 parameters should be generated automatically
if you specify LJ parameters in the atomtypes section. Check your tpr

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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