AMBER Archive (2005)

Subject: AMBER: Hbonds restraints OK but Dihedral restraints not applied

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Mon Jan 03 2005 - 08:06:48 CST

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 

-- 
------------------------------------------------------------------
| Patrick LADAM                   |                               |
| Laboratoire CSSB                |     THE BIG BANG THEORY:      |
| UFR SMBH                        |                               |
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| Tel: 01 48 38 77 26 / 76 85     |                               |
| Fax: 01 48 38 77 77             |                               |
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