AMBER Archive (2008)

Subject: AMBER: COM RESTRAINT

From: fatima.chami_at_durham.ac.uk
Date: Thu May 22 2008 - 07:17:09 CDT

Dear Amber users,
I set up the following restraint between the centers of mass of two residues,
each contains 37 atoms.
Sander failed to read this file with an output error as:
Restraints will be read from file: dist.RST
Here are comments from the DISANG input file:

 Error: No atom 01 in residue 1
***********************************************

I copied here the restraint file and I dont know what went wrong

any help please

best wishes
Fatima

# test of restraint
 &rst iat=-1,-1, nstep1=3000, nstep2=0,
    iresid=1, irstyp=1, ifvari=1,
    r2 =0.5, rk2= 5000., r2a=3.,
    igr1 = 1,1,1,1,1,1,1,1,1,1,1,1,1,1,
    1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
    1,1,1,1,1,0,
grnam1(1)='C3',grnam1(2)='H7',grnam1(3)='C2',grnam1(4)='H6',grnam1(5)='C1',grnam1(6)='S',grnam1(7)='O',
 
grnam1(8)='O5',grnam1(9)='O6',grnam1(10)='C',grnam1(11)='H9',grnam1(12)='C5',grnam1(13)='H8',grnam1(14)='C4',
 
grnam1(15)='N',grnam1(16)='H5',grnam1(17)='N1',grnam1(18)='C6',grnam1(19)='C7',grnam1(20)='C15',grnam1(21)='C14',
  
grnam1(22)='C13',grnam1(23)='C12',grnam1(24)='H1',grnam1(25)='S1',grnam1(26)='01',grnam1(27)='O3',grnam1(28)='O4',
  
grnam1(29)='H2',grnam1(30)='H',grnam1(31)='C8',grnam1(32)='C9',grnam1(33)='H4',grnam1(34)='C10',grnam1(35)='H3',
    grnam1(36)='C11',grnam1(37)='O2',
    igr2 = 2,2,2,2,2,2,2,2,2,2,2,2,2,2,
    2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
    2,2,2,2,2,0,
grnam2(1)='C3',grnam2(2)='H7',grnam2(3)='C2',grnam2(4)='H6',grnam2(5)='C1',grnam2(6)='S',grnam2(7)='O',
grnam2(8)='O5',grnam2(9)='O6',grnam2(10)='C',grnam2(11)='H9',grnam2(12)='C5',grnam2(13)='H8',grnam2(14)='C4',
 
grnam2(15)='N',grnam2(16)='H5',grnam2(17)='N1',grnam2(18)='C6',grnam2(19)='C7',grnam2(20)='C15',grnam2(21)='C14',
  
grnam2(22)='C13',grnam2(23)='C12',grnam2(24)='H1',grnam2(25)='S1',grnam2(26)='01',grnam2(27)='O3',grnam2(28)='O4',
  
grnam2(29)='H2',grnam2(30)='H',grnam2(31)='C8',grnam2(32)='C9',grnam2(33)='H4',grnam2(34)='C10',grnam2(35)='H3',
    grnam2(36)='C11',grnam2(37)='O2'
 /

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