[gmx-users] trjconv -s

[Samuel Bowerman]

That all depends on what kind of analysis you are trying to do.  Many
functions that require a '-s' structure flag also accept PDB files as
structure files, so you should be able to get by with just your PDB file.
If any of the programs give you an issue, it's probably a result of a
difference in naming convention between gromacs libraries and the CHARMM FF
that you use.

On Tue, Sep 16, 2014 at 10:28 AM, xy21hb <xy21hb at 163.com> wrote:

>
>
>
> Thanks for all the help. however, is there any way I can generate a .tpr
> file so that I can use my traj in gromacs for further analysis?
>
>
> Best,
>
>
> Yao
>
>
>
>
>
>
>
>
>
>
> At 2014-09-16 11:13:03, "Samuel Bowerman" <sbowerma at hawk.iit.edu> wrote:
> >Yao,
> >
> >There is a tool that comes with VMD called "catdcd".  You can call it from
> >the command line and convert it with minimal effort.  See here:
> >http://www.ks.uiuc.edu/Development/MDTools/catdcd/
> >
> >Take care,
> >Sam Bowerman
> >
> >On Tue, Sep 16, 2014 at 9:05 AM, xy21hb <xy21hb at 163.com> wrote:
> >
> >> Dear all,
> >>
> >>
> >> I have a .dcd trajectory with .psf from NAMD and would like to convert
> the
> >> trajectory to
> >>
> >> GMX format .gro or .trr by using trjconv.
> >>
> >>
> >> Would it be possible to do this without generating .tpr?
> >> If not, I wonder what other possible ways would be.
> >> Thanks,
> >>
> >>
> >> Yao
> >>
> >>
> >>
> >>
> >>
> >> At 2014-09-16 09:59:45, "Mark Abraham" <mark.j.abraham at gmail.com>
> wrote:
> >> >On Tue, Sep 16, 2014 at 3:51 PM, xy21hb <xy21hb at 163.com> wrote:
> >> >
> >> >> Dear all,
> >> >>
> >> >>
> >> >> .tpr in trjconv is supposed to be optional, but it is in fact
> required.
> >> >>  Any thoughts about that?
> >> >>
> >> >
> >> >Ahem "in fact required for what I am trying to do" ;-) trjconv will
> insist
> >> >on a .tpr file if you ask it to do something that needs information it
> can
> >> >only get there. But since you haven't told us your trjconv command, or
> any
> >> >detail below, then we can't really help.
> >> >
> >> >Mark
> >> >
> >> >I have a .dcd trajectory and .psf from NAMD and would like to convert
> to
> >> >> GMX format.
> >> >>
> >> >>
> >> >> Thanks,
> >> >>
> >> >>
> >> >> Yao
> >> >> --
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