From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Oct 23 2006 - 12:20:41 CDT
Hi,
I would really appreciate if you could tell me how you do your internal
coordinate restraints with tcl scripts.... Can you do constrainst on
dihedrals so as to affect the secondary structure as you want?
As for using NAMD, I do it from within free energy calculations (with
'freeEnergy on'). I use the option 'freeEnergyConfig phi_restr.inp', where
my restraint file for phi dihedral contains:
urestraint {
dihe (VAL8, 3, CA) (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) barr=100 ref=-70
dihe bound (VAL8, 3, CA) (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) gap=80
low=-120 hi=-67 delta=10
# For every peptide bond
}
mcti {
task = stepup
equiltime = 1ps
accumtime = 1ps
numsteps = 1
print = 1ps
}
The problems and issues:
1) This is taking the peptide to completely wierd regions, and NOT near -70
degrees (which is my reference).
2) How can I constrain both phi and psi so that I get the seconary structure
I want?
Suggestions are appreciated.
Thanks,
Neelanjana
On 10/23/06, Luca Bellucci <bellucci14_at_unisi.it> wrote:
>
> Hi,Neelanjana
> You can tell me how can I do restrain file?
> I do not know this method for restrain internal coordinate in NAMD
> program.
> I thought that restrain in internal coordinates could be put only with tcl
> script...tclforce etc..
> Thank you
>
> Luca
>
-- **************************************** Neelanjana Sengupta, PhD student Dept. of Chemistry Univ. of California-Irvine Irvine, CA 92697 USA Phone: 1-949-824 9921 email: sengupta_at_uci.edu ****************************************
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