AMBER Archive (2009)

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

From: Han Zheng (zhenghan403_at_gmail.com)
Date: Tue Oct 27 2009 - 17:47:20 CDT

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: amber-bounces_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(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. *
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