AMBER Archive (2007)

Subject: AMBER: Distance Restraints

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Wed Jan 03 2007 - 14:29:26 CST


Dear Amber Users,
 
 Now I am trying to put the "Leu-NH & Hb" distance restraints in the MD calcuations. Hb includes 2 H atoms. Here is the atoms that I want to add the restraints:
   resid 1-5: H118 with resid 1-5: H140, H141 2.00 5.00
   resid 1-5: H79 wtih resid 1-5: H101, H102 2.00 5.00
   resid 1-5: H40 with resid 1-5: H62, H63 2.00 5.00
   resid 1-5: H with resid 1-5: H22, H23 2.00 5.00
 I need to specify the restraints between H118 and H140, H141 intra-residue, then average these 5 residues results.
 
 Here is the DISANG file:
 # Leu-NH & Hb
  &rst iat=-1,-1, iresid=1,
   r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
   rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
   igr1 =1,2,3,4,5, grnam1(1) = 'H118',
   igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H140', grnam2(2)='H141',
 /
  &rst iat=-1,-1, iresid=1,
   r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
   rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
   igr1 =1,2,3,4,5, grnam1(1) = 'H79',
   igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H101', grnam2(2)='H102',
  /
  &rst iat=-1,-1, iresid=1,
   r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
   rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
   igr1 =1,2,3,4,5, grnam1(1) = 'H40',
   igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H62', grnam2(2)='H63',
  /
  &rst iat=-1,-1, iresid=1,
   r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
   rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
   igr1 =1,2,3,4,5, grnam1(1) = 'H',
   igr2 =1,1,2,2,3,3,4,4,5,5, grnam2(1)= 'H22', grnam2(2)='H23',
  /
 
 Do you think it is correct to realize what I want for the restraints? Thanks a lot for your any suggestion and help!
 
 All the bests,
 
 

Esther B.

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