AMBER Archive (2008)

Subject: AMBER: problem with distance restraints

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Thu Mar 20 2008 - 05:13:31 CDT

Respected amber users,
      I am using Amber 9 version. My system contain 200 residues and pdb
file is looking like as follows-
ATOM 1 O2 UUU 1 28.150 43.479 29.591 1.00 0.00
ATOM 2 P1 UUU 1 27.455 42.523 28.544 1.00 0.00
ATOM 3 O3 UUU 1 26.758 41.573 27.458 1.00 0.00
ATOM 4 O4 UUU 1 28.227 41.263 29.145 1.00 0.00
ATOM 5 O5 UUU 1 24.227 42.533 27.845 1.00 0.00
TER
ATOM 6 C7 MOL 2 31.401 42.908 31.702 1.00 0.00
ATOM 7 H10 MOL 2 31.896 42.283 32.238 1.00 0.00
ATOM 8 1H1 MOL 2 30.506 42.982 32.042 1.00 0.00
ATOM 9 2H1 MOL 2 31.829 43.767 31.734 1.00 0.00
TER
ATOM 10 O2 UUU 3 28.150 43.479 29.591 1.00 0.00
ATOM 11 P1 UUU 3 27.455 42.523 28.544 1.00 0.00
ATOM 12 O3 UUU 3 26.758 41.573 27.458 1.00 0.00
ATOM 13 O4 UUU 3 28.227 41.263 29.145 1.00 0.00
ATOM 14 O5 UUU 3 28.663 42.765 27.521 1.00 0.00
TER
ATOM 15 C7 MOL 4 31.401 42.908 31.702 1.00 0.00
ATOM 16 10 MOL 4 28.227 41.263 29.145 1.00 0.00
ATOM 17 1H1 MOL 4 30.506 42.982 32.042 1.00 0.00
ATOM 18 2H1 MOL 4 31.829 43.767 31.734 1.00 0.00
..................................

I want to keep distance restraint on atoms P1- O2, P1- O3,P1-O4 and P1-O5 in
all the residues.I used the following input and RST file.....
&cntrl
   imin=1,maxcyc=1000,ncyc=500,cut=10.0,ntb=1,nmropt=1
  &end
  &wt type='REST' , istep1=0,istep2=250,value1=0.1,
            value2=1.0, &end
  &wt type='REST' , istep1=251,istep2=1000,value1=1.0,
            value2=1.0, &end
  &wt type='END' &end
  DISANG=RST.dist

&rst iat(1)=-1,-1,r1=1.54,
  r2=1.60,r3=3.00,r4=3.50,
  rk2=40.0,rk3= 40.0,
  iresid=1,igr1(1)=1,3,5,............213,215,0
  GRNAM1(1)='P1'
  GRNAM1(1)='O2',GRNAM1(1)='O3',GRNAM1(1)='O4',GRNAM1(1)='O5'

but minimization is not running. Not reading the RST file. Please help me..

Thanks in advance
Aneesh

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