Hello Marie-Laurence--
>
> I'm currently trying to calculate the structure of a covalently linked
> homodimer using xplor v2.33 on Ubuntu 10.04 using only distance , talos
> dihedrals, and h-bond restraints.? At some point during the calculation,
> there's an error that appears (shown below) about the step size being too
> large then too small.? I'm essentially using the same parameters as the
> anneal.py found in the eginput>gb1_rdc example in the xplor package.? I have
> also used the same anneal.py file for the monomeric protein and everything
> worked smoothly.? The only difference between the monomeric and dimeric
> protein is the number of restraints, which is doubled.
>
> ?MAKINB: mode?? 3 found? 15831 exclusions,?????? 0 interactions(1-4) and?
> 15831 GB exclusions
> ?MAKINB: mode?? 3 found????? 0 exclusions,?????? 0 interactions(1-4) and?????
> 0 GB exclusions
> *--- Dynamics ---- step=????? 0 ---- time=???????? 0 ---- delta_t= 0.0015999
> --*
> | E(kin)+E(poten)=???? 20989.468 E(kin)=????? 6974.370 temperature=??
> 3457.795 |
> |?? E(poten)= 14015.0982135?????? grad=??? 67.5665364????? ANGL=?
> 2326.9185219 |
> |?????? BOND=???? 9.1756895?????? CDIH=? 2906.9832523????? HBDA=????
> 8.1348803 |
> |?????? IMPR=? 3231.5519843?????? RAMA=??? -0.5304373?????? VDW=?
> 3770.5403615 |
> |??????? noe=? 1762.3239610??????????????????
> ????????????????????????????????? |
> *------------------------------------------------------------------------------*
> InternalDynamics::step: large timestep detected. Halving.
Could you please try replacing the RAMA term with the newer torsionDB
term. Setup in your script should be:
from torsionDBPotTools import create_TorsionDBPot
torsionDBPot = create_TorsionDBPot('tDB')
potList.append( torsionDBPot )
rampedParams.append( MultRamp(.002,2,"torsionDBPot.setScale(VALUE)") )
Hopefully, this will solve the problem...
best regards--
Charles
