[gmx-users] Prevent protein rotation - rectangular box

[Justin Lemkul]

On 6/3/14, 10:14 PM, Steven Neumann wrote:
> Thanks, unfortunately I have such restrictions.
>
> I have defined two atoms which I wish to be dummy in my system. I placed
> one in between 2 beta sheets on the one termini of my protein and copy it
> moving along the z axis to the other beta sheet. I found closest prtoein
> heavy atoms and made constraints with 2 dummy atoms. In my topology :
>
> atomtypes.atp
>
> DUM    0.0000   ; Dummy atom
>
> ffnonbonded.itp (Charmm so all vdwd are turnedd of with them)
>
> DUM    1    00.0000    0.00    V    0.0000000    0.0000000
>
>
> aminoacids.rtp
>
> [ DUM ]
>   [ atoms ]
>          DUM       DUM      0.0  0
>
>
> Then, after pdb2gmx I add both constraints between dummies and closest
> protein heavy atoms (4 or 6) and add:
>
>   [ angle_restraints_z ]
>   ; i    j    funct    phi    kc    n
> 6141    6142    1    0    100    1
>
> So the angle between Z axis and two of them is zero with low force constant
> - that will prevent protein from the rotation.
>
> grompp with frozen dummies in all directions I got the error that DUM atoms
> have a zero mass. Isnt it possible to have atoms with zero masses like
> dummies? Shall I add a mass of 0.0000001 or would you suggest something
> else? Maybe I should apply [ virtual_sites ] option?
>

If you're using [angle_restraints_z], I don't see the need for a dummy atom at all.

Virtual sites may work, but again I don't know if that's the most 
straightforward approach.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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