What format are you choosing when you load the coordinates
(output.mdcrd) into VMD?
On Wed, Oct 3, 2018 at 1:42 PM Aashish Bhatt <aashish.ph16221.inst.ac.in> wrote:
>
> NAMD dcd file contain information of coordinates. Unit cell information is
> in different file name is xsc.
> Is there any other way to save file with coordinates and peroidic box?
>
> On Wed, Oct 3, 2018 at 10:55 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Does the trajectory have unit cell information? Are you perhaps
> > loading as Amber Coordinates and not Amber Coordinates with periodic
> > box?
> > On Wed, Oct 3, 2018 at 1:12 PM Aashish Bhatt <aashish.ph16221.inst.ac.in>
> > wrote:
> > >
> > > I have downloaded cpptraj from GitHub and version is v18.01.
> > >
> > > Regards
> > >
> > > Aashish
> > >
> > > On Wed, 3 Oct 2018, 10:24 p.m. Daniel Roe, <daniel.r.roe.gmail.com>
> > wrote:
> > >
> > > > What version of cpptraj are you using?
> > > >
> > > > On Wed, Oct 3, 2018 at 10:53 AM Aashish Bhatt <
> > aashish.ph16221.inst.ac.in>
> > > > wrote:
> > > >
> > > > > Dear Amber User
> > > > >
> > > > > I have NAMD dcd trajectory file and i want to convert namd dcd into
> > > > amber
> > > > > mdcrd file.
> > > > > When i try the command :
> > > > >
> > > > > http://archive.ambermd.org/201703/0206.html
> > > > > cpptraj -p <topology> -y <input dcd> -x output.mdcrd
> > > > >
> > > > > The command is running but my structure is deforming.
> > > > >
> > > > >
> > > > > Regards
> > > > > Aashish
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Received on Wed Oct 03 2018 - 11:30:03 PDT
