Can you send me the output file off list?
Carlos
On Thu, Nov 29, 2018, 8:32 AM M. Reza Ganjalikhany <ganjalikhany.gmail.com
wrote:
> Dear Carlos,
>
> As my structure has a large and complicated conformational change along two
> axes, I am not sure whether TMD is enable of simulating such transition in
> a low energy path or just move the structure to lower the RMSD value
> regardless of any other parameters.
>
> Both cases (ntr=1. restrantmask) and (ntr=0 and tgtfitmask) worked with a
> slight difference. The output shows it recognizes the masks as reported
> below:
>
> 5. REFERENCE ATOM COORDINATES
>
> defa
> Mask :1-114,131-166,188-204,229-249,448-577.CA; matches 318 atoms
> Mask ":115-130,167-187,205-228,250-447,578-775.CA" matches 437
> atoms
>
> As you mentioned, I used cpptraj to see the changing in the RMSD value. It
> decreased until the half and then it increased slowly as it could not find
> the final position. The decrease is due to the movement of N-terminal
> domain to the reference structure but it should rotate to fit the target.
> It seems that the combination of these two movement is not possible at the
> same time.
> Also, I have tested bigger force constants and the result was not really
> desirable as the structure denatured during the movement.
>
> Here are the links to some visualized trajectories:
> https://www.dropbox.com/s/weezo4c1hmoc68j/TMD1.mp4?dl=0
> https://www.dropbox.com/s/htjdlyuohlglxt5/TMD2.mp4?dl=0
> https://www.dropbox.com/s/j7idltd4ax0iaw1/TMD5.mp4?dl=0
>
> On Tue, Nov 27, 2018 at 12:24 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > also your force constant is really small
> >
> > On Mon, Nov 26, 2018 at 3:52 PM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > see section 20.4 of the Amber18 manual - you should be using tgtfitmask
> > > and tgtrmsmask but I only see tgtrmsmask in your input.
> > > I'm not sure what would happen when you also turn on positional
> > restraints
> > > as you have done here (using ntr=1 and restraintmask)- it might work,
> but
> > > it might not depending on how that matches the other masks. I don't
> have
> > > the ability to check the code right now.
> > > what does the beginning of the output say about the targeted md part?
> > does
> > > it give a fitmask?
> > >
> > > to check and see if it's working, the best way is to use cpptraj to do
> > the
> > > rmsd fit to the same reference structure that you gave the md code,
> using
> > > the same mask as you use for tgtfitmask, and then calculate the rmsd
> next
> > > using the tgtrmsmask but including the "nofit" flag. The resulting data
> > > stream should match what you asked the md to do (though it's unlikely
> > that
> > > it can reach exactly 0 rmsd).
> > >
> > >
> > > On Mon, Nov 26, 2018 at 3:22 PM M. Reza Ganjalikhany <
> > > ganjalikhany.gmail.com> wrote:
> > >
> > >> Dear Amber users,
> > >>
> > >> I am trying to run targeted MD to study a large conformational change
> > >> during the simulation between two states of a protein. As I check the
> > >> movies from the trajectories, I see that the structure moves from
> > initial
> > >> to the final structure, but it does not stop at the final point and it
> > >> continues to move further beyond the final position. Also, the moving
> > part
> > >> of the structure hits other parts of the protein and I realize that
> this
> > >> movement will not show the low energy path between the initial and
> final
> > >> conformations.
> > >> I have changed the parameters but I couldn't solve the problem. Since
> I
> > >> performed short simulations to see the results quickly, I am not sure
> > >> whether I have to set large number for *nstlim *or reduce the *tgtfrc
> ?
> > >> *Is
> > >> there any other parameter which is neglected or should be defined in
> the
> > >> input file? The input file has been attached. I wanted to send the
> > movies
> > >> but it is not possible due to the limitation is the email size.
> > >>
> > >> I appreciate you valuable comment to tackle this problem.
> > >>
> > >> Regards,
> > >>
> > >> Input parameters for targeted MD:
> > >> TMD icl2
> > >> &cntrl
> > >> imin = 0, ntx = 1, nstlim = 12000, irest=0, dt = 0.002, ntc = 2,
> ntf =
> > >> 2,
> > >> tol = 0.000001, tempi = 100.0, temp0 = 300.0, cut = 10.0,
> > >> ntpr = 10, ntwx = 10, ntwr = 100, ntb = 0, ntt = 1, tautp = 0.5,
> ntp =
> > >> 0,
> > >> igb = 1, nscm = 0, nmropt = 1, ntr = 1, restraint_wt=0.02,
> > >> itgtmd = 1, tgtrmsd = 39.553, tgtmdfrc = 0.005, restraintmask=
> > >> ":1-114,131-166,188-204,229-249,448-577.CA"
> > >> tgtrmsmask= ":115-130,167-187,205-228,250-447,578-775.CA",
> > >> /
> > >> &wt
> > >> TYPE='TGTRMSD', istep1=1, istep2=8000,
> > >> value1 = 0.0500, value2 = 0.0,
> > >> /
> > >> &wt
> > >> TYPE='TGTRMSD', istep1=8000, istep2=12000,
> > >> value1 = 0.0, value2 = 0.0,
> > >> /
> > >> &wt
> > >> type="END",
> > >> _______________________________________________
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> > >>
> > >
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Received on Thu Nov 29 2018 - 15:00:03 PST
