VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Jun 13 2009 - 17:00:27 CDT

On Wed, 2009-06-10 at 10:00 -0500, Chetan Mahajan wrote:
> Thanks, Axel.

chetan,

> 2. Regarding my point 1 of resid tool, I just followed following
> instructions in lmp2vmd README.
>

[...]

> lmpresidfromdata [molinfo top] data.micelle
>
>
>
> Since I don’t see any visible changes, I was wondering what it does,
> in particular.

i am confused. the README file gives a _detailed_ and _complete_
explanation under point 2a. which part did you not understand?

> Another little thing is I find that the step "To then add the residue
> information to a PSF file, see the steps for from
>
> item 1 from above and" not needed, since we want to generate .psf file
> with all the features of bonding, residue, atom names etc, if we
> repeat this " " step everytime for all 4 steps in lmp2vmd README, then
> final .psf file is not inclusive of all features. And since we want to
> load only one .psf file with lammps trajectory, it's not desirable to
> repeat that step of loading lammps traj every time. So I suggest
> removing those instructions from README.

sorry, but you are making even less sense here. i don't see any text
that can be removed without losing useful and important information.
please re-read the README file carefully. if you still believe that
there is misleading information, then please send me a corrected or
otherwise amended file.

thanks,
   axel.

>
>
> Thanks
>
> Chetan
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.