It says 'Cannot read file of type netcdf', and NetCDF is not an option when
using graphic interface. I changed ioutfm to 0 to see what happens.
Hopefully it will work.
Best,
Wenze Gu
Department of Chemistry
Brown University
On Fri, Mar 2, 2018 at 5:57 PM, koushik kasavajhala <
koushik.sbiiit.gmail.com> wrote:
> 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
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Received on Sat Mar 03 2018 - 07:00:03 PST
