Dear AMBER users,
I got many answers regarding my query in archive like r1 rk are sticky
values being used for all once defined at top of RST file.
But I didnt find how to give chirality and trans peptide restraint for
nonstandard residues, if I want to anneal system at 1500K. Can I use (I
mean to say is it correct?) same format of RST file as that
created by makeCHIRAL_RST command for normal protein pdb, then what
value of force constant should be used . does it depend on hit and
trial method to prevent inversion and trans to cis peptide..
>Dear Dr. Jason,
>Thanks for reply
>This is a flat-well potential described in the manual
Sorry this was new to me thats why I asked in hurried mann
two more querries please,,
1) I used makeCHIR_RST for two, three different pdb files and got this
result only r1=150., r2=170., r3=190., r4=210., rk2 = 50.,
rk3=50., &end only. Is this same for all proteins and it was
written once at top of rst file like this (does that mean all peptide
bonds will use these values)
# trans-omega constraint for residue 2
&rst iat=23,22,3,2,
r1=150., r2=170., r3=190., r4=210., rk2 = 50., rk3=50., &end
# trans-omega constraint for residue 3
&rst iat=35,34,24,23, &end
# trans-omega constraint for residue 4
&rst iat=51,50,36,35, &end
2) Can I use these values ((r1=150., r2=170., r3=190., r4=210., rk2 =
50., rk3=50)) for my nonstandard residue joined by peptide bond.. by
defining atoms
On Fri, Apr 16, 2010 at 7:15 AM, Jio M <jiomm.yahoo.com> wrote:
> Dear users,
> I have joined chiral residue with a peptide bond
> another residue. As I did annealing the configuration changed at the
> chiral center as expected. So I want to apply chiral restraints to th
> chiral center and want peptide bond to be trans
> I have seen by command make_CHIRAL_RST for normal protein pdb.
>
> &rst iat=23,22,3,2,
>
>
> r1=150., r2=170., r3=190., r4=210., rk2 = 50., rk3=50., &end
>
This is a flat-well potential described in the manual. Values between
r1 and r2 have a harmonic restraint with force constant equal to rk2.
Values between r2 and r3 have no restraint. Between r3 and r4 have a
harmonic restraint with force constant rk3. The restraints before r1
and after r4 are linear and adjusted so that the total restraint
potenial is continuous (for both the original function and 1st
derivative if I'm not mistaken).
>
>
> I am not able to get meaning of r1 r2 etc. If I am not wrong iat
> represents atom number and also they represent CA-N(of first amino
> acid)-C-CA (of second amino acid) that is CA-N--C-CA the peptide bond.
> Can I similarly do for my residues. What about r1, r2 r3 here???
You can put any atoms you want here. Again, this section (NMR
restraints) is gone over in quite a bit of detail in the amber manual.
Good luck!
Jason
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Received on Sun Apr 18 2010 - 02:00:02 PDT
