Hi all and Happy 2005,
I use amber 7 on a Linux Box and I have a serious problem applying
dihedral angle restraints during a minimization on a 20 mer DNA.
My RST file contains both Hydrogen Bonds and dihedral angles restraints
on the Backbone (ALPHA, BETA...).
I can see that the H-Bonds restraints work OK (the two strands are far
apart at the start and close to each other at the end with correct
Watson-Crick H-Bonds).
Strangely the dihedral restraints do not seem to work at all even if I
run the minimization with great number of iterations.
The output from SANDER shows a correct number of restraints read from
the RST file.
Here are my min.in script that I launch with:
sander -O -i min.in -o min.out -p dna.top -c dna.crd -r dna_min.rst -x
dna.trj -e dna.ene
&cntrl
imin=1,
ntx=1,
irest=0,
ntpr=50,
ntf=1,
ntb=0,
cut=9.0,
nsnb=10,
ntr=0,
maxcyc=20000,
ncyc=10000,
ntmin=1,
nmropt=1,
&end
&wt type='REST',
istep1=0,
istep2=1000,
value1=1.0,
value2=1.0,
&end
&wt type='END'
&end
LISTOUT=POUT
DISANG=ALPHA_Backbone.rst
Group input for DNA restraints: 0 kcal/mol.
0.0
RES 1 20
END
END
------------
Here is also a part of my RST file:
# 2 ADE ALPHA: (1 DT5 O3*)-(2 DA P)-(2 DA O5*)-(2 DA C5*) -70.0 -60.0
&rst iat = 30, 31, 34, 35,
r1 = -71.0, r2 = -70.0, r3 = -60.0, r4 = -59.0,
rk2 = 32.0, rk3 = 32.0, &end
# 3 GUA ALPHA: (2 DA O3*)-(3 DG P)-(3 DG O5*)-(3 DG C5*) -70.0 -60.0
&rst iat = 62, 63, 66, 67,
r1 = -71.0, r2 = -70.0, r3 = -60.0, r4 = -59.0,
&end
# 4 GUA ALPHA: (3 DG O3*)-(4 DG P)-(4 DG O5*)-(4 DG C5*) -70.0 -60.0
&rst iat = 95, 96, 99, 100,
r1 = -71.0, r2 = -70.0, r3 = -60.0, r4 = -59.0,
&end
Does anyone have a clue?
Thank you
--
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| Patrick LADAM | |
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Received on Mon Jan 03 2005 - 14:53:00 PST
