Hi Balaji,
> thank you Ross!
> it worked
> the force was too ohigh
> if i decrease its doing good
> but when time goes on
> the current rmsd value is not changing
> too much it stays to a particular value
> and after that the rmsd is not decreasing !
> what one have to check for it !
This may mean that the force constant is now not high enough and that you
have reached some kind of energy barrier for which there is not enough
impulse in the system to overcome it. Hence you may need to play about with
this value until you find a suitable median. This is one of the problems
with targetted MD - you almost have to know the answer before you can
calculate it.
> if one like to mask the atoms of his interest
> suppose i would like to mask 21-30 or
> some specific of like 2,3,8,40
> how to give the flag in the
> mask option
I believe (off the top of my head) that you would just do something like:
":2,3,8,40.CA,C,N,O" to select say all backbone atoms in residues 2,3,8 and
40. There are also more complex examples you can use since you can do things
like "(:2.CA | :3.N | :4.O)" which would mean the CA of residue 2 'or' the N
of residue 3 'or' the O of residue 4 - the 'or' here is passed by the mask
code so this would ultimately select all 3 of these atoms. Check section
11.3 of the amber 10 manual which describes this in detail. You can also use
the standalone ambmask code to pass your mask strings and dump the atom
selection for you to check it before running simulations.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sat Feb 28 2009 - 08:48:06 PST
