[gmx-users] positional restraint
alokjain at iitk.ac.in
Tue Nov 30 18:18:34 CET 2004
hello Xavier and David,
I am really sorry for the mistake
i made with my previous mail.The residue in question is really ASN.And
the OD1 atom is not protonated as i said in my previous mail.It was a
blunder mistake on my part to say so.The H-OD1 distance mentioned is
actually the distance between OD1 and the backbone Hydrogen 'H' of ASN.
And the distances mentioned is in Angstrom not in nanometer.
So coming back to my main question
about positional restraint.As I have shown the data that even with very
high force constant value (100000),there still is marked change in the
distances between the atoms.And the atoms are not freezed as u have
mentioned.Please shed some light into the whole issue.
Sorry for the mistake :( with my previous mail.
Xavier Periole wrote:
> David wrote:
>> 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
>>> 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
>>> between the other atoms of the protein as i expect it to vary anyway
>>> 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
>>> 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
>>> 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.
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