Thanks Carlos for your valuable input, yes i did a sample run for 50 ps and
got the results. But with the same input for 10ns, this is the situation.
FYI, i am running amber 11.11.7 rmsd is the figure for those 30 residues
mentioned in tgtfitmask. Moreover i want to pick one intermediate structure
and yes i am interested to fetch the transition path too. please suggest,
where i have gone wrong?
On Wed, Mar 4, 2015 at 5:43 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Have you previously used tmd and gotten output? For this system? Have you
> run md and gotten output? It would help troubleshoot if we knew more.
>
> Unrelated to the output file, I am not confident that the calculation you
> have in your mdin will succeed. Going from 11.7 rmsd to 0 in 20ns is a huge
> sampling problem, and the tmd doesn't really solve that. You're very likely
> to create a compact misfolded structure along the way that cannot be
> further improved due to clashes, but the restraints won't allow it to
> unfold. For example, there are many 5A rmsd structures, but not all of them
> can be turned into 0A structures without the rmsd going up first.
> On Mar 4, 2015 5:44 AM, "Pallavi Mohanty" <pallavipmohanty.gmail.com>
> wrote:
>
> > Hello Users,
> > I have come across a weird problem. I am running TMD for 10ns wherein the
> > rms difference between both the structure is 11.7 Å. Here is my input
> file
> > &cntrl
> >
> > imin=0, ntx=5, nstlim=5000000,
> > irest=1,
> > dt=0.002, ntc=2, ntf=2,
> > tol=0.000001,
> >
> > temp0=300.0,
> > ntpr=5000, ntwr=5000,
> > ntwx=5000,
> > ntb=0, ntt=1, tautp=0.5,
> > ntp=0,
> >
> > cut=16.0,
> > igb=1, nscm=0,
> > nmropt=1,
> > itgtmd=1, tgtrmsd=11.7,
> > tgtmdfrc=1.0,
> > tgtfitmask=":1-30.CA,N,C,O",
> >
> > tgtrmsmask=":1-30.CA,N,C,O",
> >
> >
> > /
> >
> > &wt
> >
> > TYPE='TGTRMSD', istep1=1, istep2=4000000, value1=11.7, value2=0.0,
> > /
> > &wt
> >
> > TYPE='TGTRMSD', istep1=4000000, istep2=5000000, value1=0.0, value2=0.0,
> > /
> > &wt
> >
> >
> > type='END'
> >
> > /
> >
> > Though the run is successfully updating the mdcrd and mdinfo file but the
> > out file is blank. What can be the possible cause?
> >
> > --
> > Regards,
> >
> > Pallavi Mohanty
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Regards,
Pallavi Mohanty
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Received on Wed Mar 04 2015 - 04:30:04 PST
