[gmx-users] Prevent protein rotation - rectangular box

[Steven Neumann]

If you use atoms which are the part of the protein being restraint with the
z axis you get artificial behaviour. If I use dummy atoms being a part of
the protein N and C domain it is not the case...


On Wed, Jun 4, 2014 at 8:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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