Hi Wenze,
Use “vmd -parm7 cfx.prmtop -netcdf md2.mdcrd” instead of the command you
used. You have ioutfm=1 set in your input file, so the final trajectory
will be a netcdf trajectory.
Alternatively, if you use the graphical interface, select Netcdf option
from the drop down menu when you load the trajectory file.
Best,
Koushik
On Fri, Mar 2, 2018 at 5:51 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > > >> > > _______________________________________________
> > > >> > > AMBER mailing list
> > > >> > > AMBER.ambermd.org
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> > > >> > >
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Received on Fri Mar 02 2018 - 15:00:05 PST
