[gmx-users] MD Error after adding a unnatural amio acid

[yuemin liu]

Hi Tsjerk Wassenaar,

I am trying to build a protein with a non-standard
amino acid by adding (covalent bond, this is what I
mean by linkage ) a bulky group (163 atoms) to the
side chain of an existing natural amino acid of wild
type protein. Energy minimization of the modified
protein had been performed in gas phase and solvent.
The solvent and whole system were also minimized and
equilibrated at different temperatures before MD
simulation. During MD, either the covalent I build or
its neighboring one got broken, and the simulation
terminated. Minimizations could not had been done if
building block is a problem, right? Following is the
line in my mdp file:
tc-grps                  = Protein_A ASO_A ASO_B SOL
NA CL

Thanks,

Liu, Yuemin
  
--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Liu yuemin,
> 
> Now I haven't got a clue of what you're trying to
> do!
> Okay, add a new group somewhere and do MD...
> 
> First of all, what is the group you're talking
> about? How did you link
> it. You mention the linkage being broken, but you're
> not doing QM;
> bonds stay bonds, but may go well out of bounds. Did
> you perform
> energy minimization? Did you check the stability of
> the group alone in
> solution?
> You talk about different groups for temperature
> coupling? Maybe give
> the tc_coupl related lines from the .mdp files? Note
> that you
> shouldn't couple such a group separately. Or do you
> mean charge
> groups? Please try to be clear on such things.
> Anyway, at this point the partial charges seem to be
> the least of your
> worries (unless you have a collection of -1,+1 or
> worse stuck
> together). I suspect your trouble is related to the
> building block.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On 1/24/07, yuemin liu <liucan1 at yahoo.com> wrote:
> > Hi Everyone,
> >
> > I once talked about this before and have new
> problem
> > now. The new group was successfully attached to
> the
> > protein, but problem comes during the process of
> MD.
> > The error messages are always like the following
> with
> > either new linkage broken or a neighboring
> Hydrogen
> > flying away. Parameters except for partial charge
> are
> > perfectly okay. The partial charges from HF
> > calculations even made it worse, because of
> different
> > scheme with gmx. I also tried to partition the new
> > bulky group into small fragments when T-coupling,
> but
> > did not help. I am wondering what the reasons are.
> Is
> > the new group too big? What is the alternative to
> > assign partial charge in gmx other than PRODRG?
> >
> > Wishes,
> >
> > Liu, Yuemin
> >     Energies (kJ/mol)
> >            Bond          Angle    Proper Dih.
> > Improper Dih.          LJ-14
> >     4.40414e+03    7.17452e+03    3.03251e+03
> > 2.44614e+03    2.21377e+03
> >      Coulomb-14        LJ (SR)   Coulomb (SR)  
> Coul.
> > recip.      Potential
> >     4.01788e+04    2.57243e+05   -1.94251e+06
> > -2.87497e+05   -1.91331e+06
> >     Kinetic En.   Total Energy    Temperature
> Pressure
> > (bar)
> >     3.45332e+05   -1.56798e+06    2.99118e+02
> > -1.03238e+01
> >
> > Shake did not converge in 1000 steps
> >     i     mi      j     mj      before       after
> > should be
> >  3173  14.01   3174   1.01     0.10000     0.15192
> > 0.10000
> > Constraint error in algorithm Shake at step 650187
> >
> >
> >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Finding fabulous fares is fun.
> > Let Yahoo! FareChase search your favorite travel
> sites to find flight and hotel bargains.
> > http://farechase.yahoo.com/promo-generic-14795097
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> list. Use the
> > www interface or send it to
> gmx-users-request at gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 









 
____________________________________________________________________________________
Finding fabulous fares is fun.  
Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.
http://farechase.yahoo.com/promo-generic-14795097