you have several choices. As Dan Roe said, DCD has some advantages. Amber
coordinates is convenient as well.
On Mon, Dec 6, 2021 at 6:18 AM ankita mehta <mehtaroadies.gmail.com> wrote:
> Hello Sir,
> Could u pls guide me which format should i convert into ?
> Which one would be best for windows and Amber simulations..
> Thanks!
>
>
> On Fri, Dec 3, 2021 at 9:50 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Fri, Dec 3, 2021 at 9:21 AM Carlos Simmerling
> > <carlos.simmerling.gmail.com> wrote:
> > > for a list of the format keywords and automatic extensions, look at
> this
> > > page:
> > >
> https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml#tab:cpptraj-trajformats
> > >
> > > there is no need to convert to dcd, pdb or other non-amber formats
> > (unless
> > > that's what you want to do, of course).
> >
> > Some points in favor of using the DCD format on windows is that being
> > binary, it will be smaller than the ASCII format and will process
> > faster. However, if you need it to be human readable for some reason
> > use the ASCII format. Make sure you are using an up-to-date version of
> > cpptraj to do the conversion (from AT21 is fine, but GitHub
> > preferred).
> >
> > -Dan
> >
> > >
> > > On Fri, Dec 3, 2021 at 5:52 AM ankita mehta <mehtaroadies.gmail.com>
> > wrote:
> > >
> > > > Hello,
> > > > I am trying to load the trajectory files .mdcrd files in vmd on
> > windows.
> > > > My simulations were run on Amber.
> > > > But everytime i load the files , the following error message is
> > displayed
> > > > on the vmd windows.
> > > > It says " problem reading the crd file".
> > > > I followed following steps:
> > > > 1. select "new molecule "
> > > > 2. Load "parm file " and select file type as "Amber parm 7".
> > > > 3. Then load the trajectory file as "mdcrd" file and select file type
> > as "
> > > > Amber coordinates' '.
> > > > 4. error message displays on the VMD windows "Problem reading CRD
> > file".
> > > >
> > > > P.S. - -I have a windows operating system.
> > > >
> > > > Any help is appreciated !
> > > >
> > > > TIA!
> > > > Ankita
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Received on Mon Dec 06 2021 - 05:00:03 PST
