Re: [AMBER] NMR distance restraints read but not used

From: Douglas Kojetin <douglas.kojetin.gmail.com>
Date: Fri, 21 May 2010 14:40:19 -0400

Setting pencut = -1.0, here are the first few distance restraints:

 --------------------------------------------------------------------------- 
---
     First atom        Last atom    curr. value target deviation  penalty
 ---------------------------------------------------------------------------
---
  HA   VAL   49 --  H    LYS   52:    3.143    4.610    1.467    0.000 d
13: 0
  HA   VAL   38 -- *HG13 VAL   38:    2.913    4.400    1.487    0.000 d
21: 0
  HA   THR   21 -- *HB3  ARG   24:    2.876    4.870    1.994    0.000 d
24: 0
  HA   THR   21 --  H    ARG   24:    3.686    4.780    1.094    0.000 d
27: 0
  HA   THR   32 --  H    GLU   35:    3.389    4.700    1.311    0.000 d
29: 0
  H    ALA   37 -- *HB3  ALA   37:    2.681    4.070    1.389    0.000 d
31: 0
The first restraint seems to be violated by 1.467, but there is no penalty
(=0).
(there is likely general problem with my input files, as these violations
are larger than I would have expected)
Doug  
On 5/21/10 2:19 PM, "case" <case.biomaps.rutgers.edu> wrote:
> On Fri, May 21, 2010, Douglas Kojetin wrote:
>> > 
>> > I am trying to perform protein structure refinement using AMBER 10
>> > (sander.MPI).  My input restraint file (DISANG.RST) contains 888 NMR NOE
>> > distance restraints and 336 torsion angle restraints (84 dihedral angles,
>> > 252 chirality restraints).  The total number of restraints = 1224.
>> > 
>> > The full output file is attached
> 
> Specific advice:
> It is probably the case that all your restraint energies are zero.  The
> summary printed at the end only prints restraints whose energy is greater than
> pencut (I think that is the name), which defaults to some positive value.
> Set pencut=-1.0 (or any negative number) to see all of the restraints in the
> summary at the end.
> 
> General advice:
> Try a serial simulation, to eliminate the possibility of specific parallel
> problems.  Don't run a many-step simulation with a thousand restraints: set up
> a 10 step run (with ntpr=1) and use a single restraint.  The command
> "LISTIN=POUT" is also useful in seeing how sander is interpreting your input.
> 
> ....dac
> 
> 
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Received on Fri May 21 2010 - 12:00:05 PDT
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