Thanks you very much!
James
2014-09-09 17:43 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Without knowing the exact error, again I can only speculate. If you
> are using a CHAMBER topology these are currently not recognized by
> VMD. In order to use it with VMD you need to strip out the CHAMBER
> information using the 'nochamber' keyword. Be aware that while this
> stripped/nochamber topology will be fine for visualization/analysis,
> it should not be used for simulations (since it is now missing
> information).
>
> One quick tip: if you're using Amber topologies with VMD a lot, name
> them with the '.parm7' extension for automatic recognition.
>
> -Dan
>
> On Tue, Sep 9, 2014 at 12:07 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > Hi Dan,
> >
> > thank you very much for the help! Indeed in the second case the problem
> was
> > due to the topology
> > BTW I've triet to prepare topologies with no box and stripped from water
> > taking command sequence from the tutorial- but the resulted topology
> could
> > not recognized by VMD.
> >
> > parm system.parmtop
> > parmstrip :WAT
> > parmbox nobox
> > parmwrite out stripped.parmtop
> >
> > Where might be error?
> >
> > James
> >
> > 2014-09-08 17:59 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >
> >> On Mon, Sep 8, 2014 at 2:45 AM, James Starlight <jmsstarlight.gmail.com
> >
> >> wrote:
> >> > 1) need to remove periodicity and wrapping from my trajectory
> >> >
> >> > trajin md.nc 1000 last 5
> >> > reference protein.inpcrd
> >> > unwrap
> >> > center :1-289 mass origin
> >> > image origin center
> >>
> >> This is not a useful command sequence and the exact opposite of what
> >> you want. You are unwrapping (i.e. removing imaging) and then
> >> re-imaging. If you want to remove wrapping just use 'unwrap'. I
> >> strongly recommend you read the manual and become familiar with every
> >> command you try to use before you run your calculations.
> >>
> >> > 2) if I chose possibility to save trajectory after RMSD fitting
> >> > trajin md.nc 1000 last 5
> >> > reference protein.inpcrd
> >> > rms reference :1-289.CA out rmsd.dat
> >> > outtraj afterRMSD.nc
> >> >
> >> > it has produced correct RMSD.dat output but no any processed
> trajectory
> >> > afterRMSD.nc has been appeared in the work dir.
> >>
> >> If you have multiple topologies specified cpptraj will try to use the
> >> first topology for 'trajout'/'outtraj' commands, and if that topology
> >> does not match the topology for the input trajectory the output
> >> trajectory will not be written. However, without seeing your complete
> >> cpptraj output I can only speculate.
> >>
> >> -Dan
> >>
> >> >
> >> > Thanks for help,
> >> >
> >> > James
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 10 2014 - 00:30:02 PDT
