AMBER Archive (2009)

Subject: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!

From: Han Zheng (zhenghan403_at_gmail.com)
Date: Tue Oct 27 2009 - 12:28:16 CDT

Dear, amber10 users,

i am trying to constrain a torsion angle which is formed by the centers of
mass of four different atom groups.
But no matter what group members i were choosing, the initial dihedral angel
in "log" file is the same wrong
value.

The different machine and compiler have been tried and came out with the
same wrong value.
I tried to constrain angle and distance which are formed by the centers of
mass of atom groups,
and the results are correct. Anyone has an idea what might cause this group
torsion constrain goes wrong?
Thanks a million!

Best,
Han Zheng

Here are my IN and RST file (tor.RST):
------------------------------
----------------------------------------------------------
minization of DNA in water
 &cntrl
  imin = 1,
  maxcyc = 50,drms=0.01,
  ncyc = 50,
  ntb = 1,
  igb = 0,
  cut = 12,
  NTR=0,
  iwrap=1
  nmropt=1,
 /
    &wt type=DUMPFREQ, istep1=1, /
     &wt type=END, /
     DISANG=tor.RST
     DUMPAVE=minrestraint.log
     LISTIN=POUT
     LISTOUT=POUT
--------------------------------------------------------------------------------------------
    &rst iat = -1, -1, -1, 0,
     r1=-180., r2=85.0, r3=85.0, r4=180., rk2 =1000.0, rk3=1000.0,
     igr1 = 513, 514,
     igr2 = 511, 512,
     igr3 = 478, 479,
     igr4 = 198, 199,
    &end
--------------------------------------------------------------------------------------------

In the output file:
Here are comments from the DISANG input file:

******
 COM ( -1)-COM ( -1)-COM ( -1)-COM ( -1) NSTEP1= 0
NSTEP2= 0
 Atom ranges defining Center of Mass Group in the first position:
   513 -> 514/
 Atom ranges defining Center of Mass Group in the second position:
   511 -> 512/
 Atom ranges defining the Center of Mass Group in the third position:
   478 -> 479/
 Atom ranges defining the Center of Mass Group in the 4th position:
   198 -> 199/
R1 =-180.000 R2 = 85.000 R3 = 85.000 R4 = 180.000 RK2 =1000.000 RK3 =
1000.000
 Rcurr: 83.284 Rcurr-(R2+R3)/2: 1.716 MIN(Rcurr-R2,Rcurr-R3):
1.716
                       Number of restraints read = 1

                  Done reading weight changes/NMR restraints

It seems the group constrain has been added successfully, and the* initial
torsion angle is calculated correctly as 83.284*

But at the end of the output file:
------------------------------------------------------------------------------
     First atom Last atom curr. value target deviation penalty
 ------------------------------------------------------------------------------
 *H1' DT 17 -- *H1' DG 16: *-51.697* 85.000 136.697 5692.132 t
                                       Total torsion penalty: 5692.132
 ------------------------------------------------------------------------------

>From the minrestraint.log file:
  * 0 -51.659* *==> should be 83.284*
       1 -51.659
       2 -51.660
       3 -51.661
       4 -51.662
       5 -51.663
       6 -51.665
       7 -51.667
       8 -51.669
       9 -51.672
...
      49 -51.697

*
No matter what atom groups i chose for this dihedral angle, the initial
value in log file is always -51.659.
It seems the program recognizes the center of mass dihedral angel, but
during the minimization/dynamics,
it is calculating something else. *
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber