On Fri, Apr 29, 2011 at 3:45 PM, Samuel Genheden
<samuel.genheden.gmail.com>wrote:
> Hi
>
> I'm a PhD student with Ryde, so I felt that I should comment on this
> thread.
>
> We always use the perl script because the python script was not around
> when we started with our calculations, and we have seen no reason to
> change to the python script.
>
It's probably easier to use for newcomers, and the input is namelist-style
like many other amber programs (and does a bit more out-of-the-box as of
AmberTools 1.5 than the perl script does), but your group has plenty of time
invested in understanding (and manipulating) the perl version that would
have to be redone if you switched -- not surprising that you haven't. I
still think the python version is a good place for newcomers to *start*,
since it's a bit easier to use (in that it catches user error and doesn't
require users to input what can be determined directly from the input files)
and actively supported on this list, but that doesn't apply to people/groups
with substantial investment in the perl version.
> We use nmode for the normal mode analysis, but as far as I understand
> this program is deprecated nowadays. We had to modify the nmode
> program so that we could use a belly in the calculations (i.e. a
> buffer region). These changes are described on our homepage:
> http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html
>
> Perhaps a similar change as to be done to the normal mode analysis
> code of nab, I'm not clear if nab allows you to keep something fixed
> in NMA.
>
I don't think so, but I haven't looked at the nmode part of the nab code.
You can constrain stuff during minimizations (wcons), but I don't know how
(or if) this affects the normal mode calc. One nice thing that the nab code
has is the ability to include GB in the nmode calculation
> Also you need to have a special program to create the truncated
> trajectories for you. We have a program that goes through a
>
Why? Will ptraj not work?
trajectory, truncates it + a number of water molecules, and print a
> file for each snapshot. I'm sure that our program can be modified
> rather easily to get a single trajectory instead of many files.
>
I'm pretty sure ptraj will do all of that with a simple "strip" command and
a trajout to the right format (PDB, restart with an appropriately paired
prmtop, etc.)
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 29 2011 - 07:30:05 PDT
