[gmx-users] positional restraint
x.periole at chem.rug.nl
Tue Nov 30 17:12:33 CET 2004
>On Tue, 2004-11-30 at 01:32 +0530, Alok wrote:
>>hello David and Xavier,
>> Thanks for all your responses to my previous
>>mails.I am sorry,I still have to bother you with
>>some more queries about the constraint.In the
>>process i would also like to answer few questions
>>u have asked in your responding mails.
>>What is the range of differences you observe ?? Is it for the restrained
>>part or the rest of the protein ?
>>The Observed distance difference is for the restrained part (the atoms
>>from the constrained residue).I have not checked the distance difference
>>between the other atoms of the protein as i expect it to vary anyway since
>>i am constraining only one residue in my protein.
>>I present below data of distances (in Angstrom) between atoms of my
>>constained residue for the crystal structure as well as for the output
>>after Energy minimization using different Force constant.
>> (Force Constant)
>> Crystal 1000 10000 100000
>> O-OD1 2.58 3.17 2.87 2.66
>Is your OD1 protonated? It should...
It seems to me that this residue is a ASN, since it contains OD1 and
ND2. So I do not see why
the OD1 should be protonated. I must be missing something !
Although the distance is really small and should be a H-bond, which
explain certainly why David
suggested that the OD1 should be protonated. That is my guess.
Another solution is that the X-ray attributed the density of ND2 to OD1
and vis versa, That happens
as the two atoms a not nesseraly easily discernable !
>> O-HD21 4.86 5.27 5.13 4.95
>> O-HD22 4.75 5.35 5.06 4.83
>> H-OD1 4.73 4.76 4.75 4.75
>> N-HD21 4.62 4.57 4.74 4.71
>> N-HD22 5.58 5.62 5.65 5.62
>> H-ND2 4.94 4.66 4.80 4.87
>>As we can observe even after value of 1000000,the atoms have not freezed
>>as u have mentioned in your mail.
>>my corresponding ".mdp " file for EM is as follows:
>>cpp = /lib/cpp
>>define = -DFLEXIBLE
>>constraints = none
>>integrator = steep
>>nsteps = 10000
>>; Energy minimizing stuff
>>emtol = 200
>>emstep = 0.01
>>nstcgsteep = 1000
>>nstcomm = 1
>>ns_type = grid
>>rlist = 1.0
>>rcoulomb = 2.0
>>rvdw = 1.2
>>Tcoupl = no
>>Pcoupl = no
>>gen_vel = no
>>If I am not able to freeze the atoms even after such high Force Constant,
>>then i am going wrong some where as you have suggested.Can you please
>>suggest the possible reason for the problem and would be thankfull if you
>>can shed some light into the possible solution.
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
9747 AG Groningen
email: x.periole at chem.rug.nl
More information about the gromacs.org_gmx-users