[gmx-users] Prevent protein rotation - rectangular box

[Justin Lemkul]

On 6/4/14, 11:20 PM, Steven Neumann wrote:
> 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...
>

I thought you said dummy atoms were causing problems.  Are you using virtual 
sites instead?  If so, I don't see how this isn't artificial as well, since the 
forces acting on virtual sites are interpolated onto their constructing atoms. 
Anything you do here is artificial.

-Justin

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

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

==================================================