Dear Carlos,
Thank you very much, I will update igb.
What you mentioned abut simulation #5 was true (temperature and initial
restraint energy). But if you check the simulation #2 the initial
restraint energy and the temperature are alright. I also believe that the
mask is a bit complicated but I have already tested other simplified masks
before.
I will run other simulations based on your recommendations to see if I can
improve the result.
Regards,
On Fri, Nov 30, 2018 at 3:59 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I only looked at the first of the output files. Some thoughts :
> - you're using igb=1,which is quite old and not a good choice for modern
> simulations
> - your initial restraint energy is huge because your initial rmsd doesn't
> match your target value. Your temperature is over 1,400 degrees. wouldn't
> trust anything that happens after that.
> - I don't really understand your atom masks. Alternating groups of residues
> in the fit and rmsd masks doesn't look like what was going on in the movie
> you sent before. I'm not sure people will be able to help you select the
> right masks since they are so project specific, but be sure they make sense
> to you.
>
> On Fri, Nov 30, 2018, 4:22 AM M. Reza Ganjalikhany <ganjalikhany.gmail.com
> wrote:
>
> > Here are the links to the outputs:
> > https://www.dropbox.com/s/lkytj6a70wpr5kc/tmd5.out?dl=0
> > https://www.dropbox.com/s/webobxahghmchs2/tmd2.out?dl=0
> > https://www.dropbox.com/s/x6ni7r1vxelextr/tmd.out?dl=0
> >
> >
> > On Fri, Nov 30, 2018 at 2:08 AM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > 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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Received on Fri Nov 30 2018 - 05:30:04 PST
