Then when you loaded the necessary file next, what exactly did VMD say?
On Mar 1, 2018 6:44 PM, "Gu, Wenze" <wenze_gu.brown.edu> wrote:
> Hi Carlos,
>
> Yes, I first loaded the prmtop file and then loaded the mdcrd file. After
> loaded the prmtop file, vmd said there are 38800 atoms.
>
> Best,
> Wenze Gu
> Department of Chemistry
> Brown University
>
> On Thu, Mar 1, 2018 at 2:37 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > this was just discussed a few days ago on the list, most likely you are
> not
> > using the right format for the file in VMD.
> > Amber coordinates format is the trajectory file (mdcrd), restart format
> is
> > the restart file. did you load your prmtop first, then the mdcrd file as
> > coordinates format (or coordinates with box)?
> >
> > On Thu, Mar 1, 2018 at 2:16 PM, Gu, Wenze <wenze_gu.brown.edu> wrote:
> >
> > > Dear list,
> > >
> > > I ran amber MD with this .in file:
> > >
> > > md, npt, equilibrium to 300K quickly,
> > > &cntrl
> > > imin = 0, ntx = 7, irest = 1, ig=-1
> > > ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0, ntwr=50000,
> > > ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
> > > nstlim = 10000000, dt =0.002,
> > > temp1=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> > > ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
> > > &end
> > > END
> > > END
> > >
> > > However, when I tried to read the trajectory file in VMD, it says
> > incorrect
> > > number of atoms <0> in mdcrd file. Meanwhile, the prmtop file has
> normal
> > > number of atoms. Do you know what's going wrong here? Thanks!
> > >
> > > Best,
> > > Wenze Gu
> > > Department of Chemistry
> > > Brown University
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Received on Thu Mar 01 2018 - 16:30:02 PST
