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 - 12:00:02 PST
