AMBER Archive (2004)

Subject: Re: AMBER: Molecular dynamic

From: bybaker_at_itsa.ucsf.edu
Date: Fri Jul 09 2004 - 17:54:38 CDT

Hello, Ross:

Thank you very much for your comments about my question on MD.

I built my protein model from a homology protein crystal structure. I
would like to build a disulfide-bond between C-terminal helix and its
adjacent loop. And to test how stable the S-S bond by running molecular
dynamic. Before doing so, I tested the running condition with native
structure to see if there are some changes. The protein is made up of
standard amino acids. There was no problem for leap to load its .pdb
file. The native protein contains 4 cycteine, but no S-S bond formed in
its 3D-structure. The template for the modeling contains 3 ‘MSE’ and 1
‘TAR’. MSE refers Selenomethionine, and TAR refers to tartaric acid. I
don’t know how these molecules got into the crystal structure. And the
auther did not mention anything about these unuausl molecules with their
crystal structure. Referring the paper, none of them were included in
the protein crystallization and purification. And I had trouble to load
the template .pdb file in leap. As Amber can’t recognize these molecules.
I did not include these moleculars with my model. The model went through
energy minimization. The unfolding only occurred when I tried to run it
with MD. It may worth to put them back to my model structure.
 
When I solvated and add ions to the structure, the program automatically
search the places to put the ions. And I have to depended the program
does the job properly. With all the .pdb file after the energy
minimization, HIS residues have been changed to HID.

The following is how the system solvated and neutralized:

> solvateBox test WATBOX216 10
  Solute vdw bounding box: 50.000 48.604 54.035
  Total bounding box for atom centers: 70.300 68.604 74.035
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 73.553 71.808 77.076 angstroms.
  Volume: 407096.264 A^3
  Total mass 197457.906 amu, Density 0.805 g/cc
  Added 9629 residues.
> charge test
Total unperturbed charge: -2.00
Total perturbed charge: -2.00
> addIons2 test Na+ 0
2 Na+ ions required to neutralize.
Adding 2 counter ions to "test" using 1A grid
Grid extends from solute vdw + 1.87 to 7.87
Resolution: 1.00 Angstrom.
grid build: 7 sec
Calculating grid charges
charges: 683 sec
Placed Na+ in test at (-10.88, -2.12, 15.09).
Placed Na+ in test at (-1.88, -5.12, 3.09).

For my understanding now, I should only allow the target regions to move
during a MD run, while the rest should be in a fixed condition. Is this
correct? To put the whole system in a MD run might generate faulse
results. And further more, I should modify the conditions to a smoother run.

As a beginner for Amber program, I find that this mail system is great!.
Thanks for providing such a place! Thank you very much for reading my
question and giving me advices.

Best regards

Bo Yang

On Thu, 8 Jul 2004 10:24:21 -0700 "Ross Walker" wrote:

> Dear Bo,
>
> > I tried to run molecular dynamic with my protein structural
> > model using Amber7.
> > After the run, I notice that there are significant changes in
> > the structure. All the helix regions became partial unfolded. A
> > beta-sheet region connecting the N-terminal helix also turns to be
> > unfolded. I checked the energy (total, potential and kinetic) levels,
> > temperature, density & volume Vs. Time (ps) of the entire MD process
> > (including equilibration and production stages). All remained
> > in stable
> > conditions after 20 ps run. And the mean pressure level is ~
> > 1 atm after
> > 50 ps. All these data indicated that I had a successful MD run.
> > Furthermore, the RMSD level steady increased at first 20 ps, and was
> > gradually increasing during the rest of the run.
>
> It is not obvious what is happening here. It may actually be possible that
> your system is actually more stable with those sections unfolded, although
> if you started from a good crystal structure this is unlikely. You don't
> mention specifically what you are simulating. Is it a protein made up of
> standard amino acids? If not how did you get the parameters for the
> non-standard parts, it could be these at fault. Also, you should check
> things like di-sulphide bridges. These are not added by default and
> must be
> manually specified. E.g Crambin will unfold if you don't add the
> disulphide
> bridges when preparing the input files in leap.
>
> It is also possible that your system is hydrogenated in an
> unfavourable way
> leading to steric clashes that result in the system "almost" blowing
> up. You
> could try running your minimisation in two stages where you initially
> minimise just the waters and counter ions with weak (~10Kcal)
> restraints on
> the protein and then do a second stage of minisation where you allow
> everything to move.
>
> Your methodology looks pretty good though. A couple of things I would
> initially try is to:
>
> 1) check your system has the correct protonation. In particular check
> histidine residues.
>
> 2) ensure your system was properly charge neutralised.
>
> 3) Try running the heating stage again but from 0K to 300K and set it to
> write to your mdcrd file every step. Then you will be able to load
> the mdcrd
> file into something like vmd and see what is initiating the
> unfolding. Does
> it look valid or does it look like it is caused by steric issues from
> hydrogenation.
>
> > From related papers on line, most of them indicated that only minimal
> > conformational change observed with their MD runs. I went
> > back to check the template used for my structure modeling. The original
> crystal
> > structure template contains three MSE residues(?) in the
> > helix regions.
>
> Did you strip these for your MD??? Do you know what MSE residues are? A
> picture would be good. I am guessing that you will need to include
> these and
> will need to obtain parameters for them, either by analogy, finding
> published parameters or by fitting.
>
> > after MD run. The MSE in the original crystal structure may have some
> > effects to stabilize the 3D-structure?
>
> Most likely... Especially if you didn't include them in your MD run.
>
> > Minimization solvates with cartesian restriantes for the solute
> > &cntrl
> > imin=1, ncyc=250, maxcyc=1000, ntpr=5,
> > &end
> > Group input for restrained atoms
> > 100.0
> > RES 1 220
> > END
> > END
>
> Try weaker restraints here - say 10KCal.
>
> > Initial molecular dynamic run 1: heating up the system, equilibration
> > stage 1:
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntt=1, tempi=100.0, temp0=300.0, tautp=2, ig=209858,
> > ntp=0,
> > ntb=1, ntc=2, ntf=2,
> > nstlim=5000, dt=0.002,
> > ntwr=5000, ntwx=5000, ntpr=500,
> > &end
>
> Set ntwx and ntpr=1 so that you can get a detailed view of what is
> happening.
>
> > (from my last question posted about MD, I learned that the
> > 'ntx' needs to
> > be set at '7')
>
> This is redundant in Amber 7 and Amber 8. NTX should normally be set to 5
> for a restart. The box info will be read automatically if the run is a
> periodic boundary run. NTX=7 is just included for backwards compatibility.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu