I don't use VMD on command line and am having trouble tracking down which
flags choose which file formats for the -cor flag. You might want to try
the VMD lists. Alternatively, you can use interactive VMD to load your
structure using the suggestions I gave before, and see what happens then. I
have more experience with that mode and it seems to work fine.
On Thu, Mar 1, 2018 at 7:20 PM, Gu, Wenze <wenze_gu.brown.edu> wrote:
> I used this command:
>
> vmd cfx.prmtop -cor md2.mdcrd
>
> And it says,
> ERROR>Error reading optional structure information from coordinate file
> md2.mdcrd
> ERROR>Will ignore structure information in this file.
> Info>Using plugin cor for coordinates from file md2.mdcrd
> ERROR>Incorrect number of atoms <0> in coordinate file md2.mdcrd
> ERROR>Mismatch between existing molecule or structure file atom count and
> coordinate or trajectory file atom count.
> Info>Finished with coordinate file md2.mdcrd.
>
> Best,
> Wenze Gu
> Department of Chemistry
> Brown University
>
> On Thu, Mar 1, 2018 at 7:02 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Sorry for the autocorrect. When you loaded the mdcrd file into that
> > molecule what did it say?
> >
> > On Mar 1, 2018 7:02 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com
> >
> > wrote:
> >
> > > 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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> > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >
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> > >> >
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> > >
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Received on Fri Mar 02 2018 - 15:00:05 PST
