Dear Deepti,
> I am trying to do the tutorial 5- The Nudged Elastic Band Approach to
> Finding the Lowest Energy Pathway Between two States
>
> and i am stuck at the addles part. The addles.out file is created but
> it is empty. moreover, the other two files neb.prmtop and neb.inpcrd
> which are supposed to form as output files are not created.
Are you sure you are using Amber 9 with all the latest bugfixes applied? I
just tried this myself using a clean copy of amber9 and the following:
Save str1.prmtop from website.
Save str1.inpcrd from website.
Save str2.inpcrd from website.
> cat str2.inpcrd >> str1.inpcrd
Save addles.in from website.
$AMBERHOME/exe/addles <addles.in >addles.out
This works fine. Also are you certain there are no error messages printed?
> another thing i would like to ask is the two end point conformations
> that are made in addles, how are they made?i mean where can one change
> the torsion angle atc to make a protein with different conformation.
> any sugguestions in this regard are welcome as i am completely stuck.
The first thing you need to realize here is that this is really a research
project in itself. The tutorial is really only designed as a brief
introduction. None of us really know yet how useful NEB is, or indeed what
is the best way to run it, where the pitfulls are etc. So you need to be
ready for this and do a lot of thinking on your own. You will likely need to
write your own software and scripts for parts of it. The way I created the
two end points was to setup amber with NMR restraints to restrain the
dihedral to the required value and then minimized the structure. Once you
have it close to the local minimum you can remove the restraints and rerun
the minimization and it should remain in the local minimum.
You could also potentially write your molecule as an z-matrix and then
convert it back into cartesian coordinates. Or just write your own script to
calculate the necessary transformation matrix and then have it write out the
necessary coordinates. In terms of providing an initial guess of the pathway
I have no idea how important this is. For large proteins I suspect it will
be necessary but don't have any quantitative experience with this.
I am sorry I can't help much more here but that is the nature of research,
you are stepping into new territory and so need to make your own decisions
about what is the best path to take - just remember - while it is hard it is
also very rewarding when things actually work...
Good luck...
Ross
/\
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
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Received on Sun Mar 18 2007 - 06:07:20 PDT
