AMBER Archive (2009)Subject: Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Oct 27 2009  18:22:43 CDT
actually there are quite a few bugs in that part, depending on exactly what
you are doing. there will be a bugfix soon, we are still checking some
parts.
On Tue, Oct 27, 2009 at 6:47 PM, Han Zheng <zhenghan403_at_gmail.com> wrote:
> thanks Matthew. I checked the source code and found out it is easy to fix
> it. Just in case
> somebody else run into the problem before the bugfix is posted.
> 
> goto /src/sander/nmr.f file: make changes in subroutine ndvprt and nmrgrp.
> line 2561: call tornrg(x, f, ...) ====> call tornrg(xcom,f...)
> line 3514: call tornrg(x, f, ...) ====> call tornrg(xcom,f..)
>
>
> best,
> Han Zheng
>
>
>
> On Tue, Oct 27, 2009 at 5:17 PM, Seetin, Matthew <
> Matthew_Seetin_at_urmc.rochester.edu> wrote:
>
> > Yes, this is a known issue. A bugfix for it should be posted soon.
> >
> > Matthew Seetin
> >
> >
> > Original Message
> > From: amberbounces_at_ambermd.org on behalf of Han Zheng
> > Sent: Tue 10/27/2009 1:28 PM
> > To: amber_at_ambermd.org
> > Subject: [AMBER] Possible bug in "com" group torsion angle constrain?
> > Thanks!
> >
> > 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(RcurrR2,RcurrR3):
> > 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
