[gmx-users] NMR Structure determination]

[Eiso AB]

Wolfram Gronwald  wrote:
>
>
>>>> spoel at xray.bmc.uu.se 12/01/04 10:07 AM >>>
>
> On Wed, 2004-12-01 at 09:27 +0100, Wolfram Gronwald wrote:
>
>> Hi,
>>
>> I am new to GROMACS and have the following question. Is it suited for
>> standard Protein NMR structure calculation starting from an extended
>> strand and if yes are there .mdp parameterfiles available to do so?
>
> Works fine. Just take care that you turn on distance restraints.
>
>>
>> Thanks a lot
>> Wolfram
>
> Hi
> Thanks for your answer this sounds good, but what parameters should I
> use? Do you have a set for NMR structure determination? In the examples
> I found parameters for doing  MD at a constant temperature in a box of
> water, but what I probably need is a simulated annealing run starting at
> e.g. 2000 K and then slowly cooling down to room temperature followed by
> a final energy minimization (at least this is what I usually do when
> using X-Plor).

Hi Wolfram,

to do simulated annealing you would have to use something like

ref_t=2000
annealing = yes
zero_temp_time = 20 (ps)

and do separate runs for the high-T, annealing and low-T stage

I have very happily used gromacs for refinement purposes, starting
from pre-folded structures.

that being said, I'm not sure that gromacs would be the best choice
if you want to generate a lot of nmr models from extended structures.
With some fiddling you would probable be able to do similar things which
distance-restraints as e.g. CNS in cartesian space and it would probable be
faster , but I don't know of anyone having done that.

There are also the following things to consider

* Torsion Angle dynamics will probably be much faster (as in e.g. cyana or CNS
or Xplor-NIH; cyana is very easy to setup; a 4 line script would get you
running, and most types of NMR data are supported).

* distance restraints and dipolar coupling (orientation) restraints are well
implemented in Gromacs, with time/ensemble averaging etc (thanks Berk!) but I'm
not sure whether dihedral angle restraints (from TALOS or J-coupling) are easily
useable from an NMR viewpoint

* as far as I know (haven't checked recently) swapping prochiral groups during
the run is cumbersome, you could probable construct a floating chirality
protocol where you remove the angle restraints temporarily but that is
probably not the best way to do it.

* there is one forcefield with hydrogens which is an adaptation of the standard
forcefield in 1998 or so, the newer versions are probably a lot better but don't
have hydrogens. this might not matter a lot if you use restraints.

* according to the ARIA or CNS manual, with uniform masses and force constants
for bonds and angles it is possible to use larger timesteps.
you would have to create your own forcefield if you want this. (but for uniform
masses and force constants it would probably be very easy to do this)

Maybe I 'm wrong about some of these points, please correct me if I am.
they are from my own experience, a few years ago. It might be that there are
more NMR specific things inplemented since then.

I have some scripts for conversion of restraints into gromacs itp format,
you can mail me if you want them.

goodluck, Eiso


>
> Thanks a lot
> Wolfram
>
>


-- 
                    _________
  _________________/ Eiso AB \___________________________

        o

              o        Dept. of NMR Spectroscopy
                       Bijvoet Center for Biomol. Research
                       Utrecht University
               o       Padualaan 8, 3584 CH Utrecht
         . .           The Netherlands
      o   ^
      |   -   _        eiso at nmr.chem.uu.nl
       \__|__/
          |            http://www.nmr.chem.uu.nl/~eiso
          |            tel: +31-30-2539929
         / \
        /   \
        |   |
  ___ ._|   |_. _________________________________________


-- 
                    _________
  _________________/ Eiso AB \___________________________

        o

              o        Dept. of NMR Spectroscopy
                       Bijvoet Center for Biomol. Research
                       Utrecht University
               o       Padualaan 8, 3584 CH Utrecht
         . .           The Netherlands
      o   ^
      |   -   _        eiso at nmr.chem.uu.nl
       \__|__/
          |            http://www.nmr.chem.uu.nl/~eiso
          |            tel: +31-30-2539929
         / \
        /   \
        |   |
  ___ ._|   |_. _________________________________________