VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed Jun 01 2005 - 01:32:33 CDT

On Tue, 31 May 2005 11:35:45 +0530 cbala_at_igib.res.in wrote:

>
> hello,

hi,

>
> I am a student from india. Just now i have started using VMD. I ran a md
> in amber.Basically i am practising amber tutorial for DNA.it has been
> given in it that loading the .prmtop and .mdcrd file of an md run in
> vmd, we can visualise the moving picture of the trajectory.
>
> when i load the .mdcrd(crd filetype) and .prmtop(parm7 file type) files
> created by amber. the no. of frames is shown as 0 and the structure is
> not getting loaded.
>
> i get a message like below
>
> "could not determine no. of atoms.please load the structure file first
> and try loading this file again."

well, the message says it all. ;-) (ok, for those who know).
the coordinate file does not contain any information about the
structure of your system, so you have to _first_ load the structure
(i.e. the topology file). since that has no coordinates, there are
0 frames. if you then load the .crd file _into_ the existing molecule,
you'll get what you want. check out the VMD users guide and the
VMD tutorials. the relationship between the .psf and .dcd files
mentioned there is about the same as with .prmtop and .mdcrd.

hope this helps,
        axel.
        
>
> i dnt understand what to do, can anyone help me what should i do.
>
> thanks in advance,
> c.bala
> igib,
> delhi, india.
> 

--
=======================================================================
Axel Kohlmeyer      e-mail:  axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                   http://www.theochem.ruhr-uni-bochum.de
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.