you have a very large number of things going on in your input. you might try
removing some of the options as a way to troubleshoot it. i don't know of a
reason the saltcon itself shuld cause problems if none exist in the rest of
your protocol (including the ligand parameters, which you don't mention).
On Thu, Feb 25, 2010 at 11:00 AM, Michael Durney <mdurney.gmail.com> wrote:
> Dear Amber users,
>
> I am running two parallel Amber calculations for (1) an RNA and (2)
> the same RNA with a small molecule ligand. The run for the free RNA
> works really well, especially when I set saltcon=0.2. Previously I had
> saltcon=0.1 and both the free RNA and the complex worked reasonably
> well but with a higher RMSD for the ensemble. When I try to switch to
> saltcon=0.2 for the complex I get a lot of vlimit exceeded message and
> the energies shoot up very rapidly to reach "NaN" and no output
> coordinates obviously. Right now I am testing higher vlimit settings
> but I know that this is not a solution since even if the run did
> finish the structures may not be relevant. I am including my input
> file below and would be grateful for any suggestions. Is it something
> to do with moving the small molecule into place which is harder at
> higher saltcon?
>
> Thanks,
>
> Michael.
>
>
> &cntrl
> nstlim=50000, pencut=-0.001, nmropt=1,
> ntpr=500, ntt=1, ntwx=200,
> cut=15.0, ntb=0, vlimit=50,
> igb = 1, iscale=10, imin=0,
> dt=0.0002, saltcon=0.2, gbsa=1,
> /
>
> &wt type='TEMP0', istep1=0,istep2=12500,value1=500.,
> value2=500., /
> &wt type='TEMP0', istep1=12501, istep2=45000, value1=500.0,
> value2=100.0, /
> &wt type='TEMP0', istep1=45001, istep2=50000, value1=0.0,
> value2=0.0, /
>
> &wt type='TAUTP', istep1=0,istep2=12500,value1=0.4,
> value2=0.4, /
> &wt type='TAUTP', istep1=12501,istep2=45000,value1=4.0,
> value2=4.0, /
> &wt type='TAUTP', istep1=45001,istep2=47500,value1=1.0,
> value2=1.0, /
> &wt type='TAUTP', istep1=47501,istep2=50000,value1=0.1,
> value2=0.05, /
>
> &wt type='REST', istep1=0,istep2=7500,value1=0.1,
> value2=1.0, /
> &wt type='REST', istep1=7501,istep2=50000,value1=1.0,
> value2=1.0, /
>
> &wt type='IMPROP', istep1=0,istep2=50000,value1=1,
> value2=250, /
>
> &wt type='BOND', istep1=0,istep2=50000,value1=1,
> value2=4, /
>
> &wt type='ANGLE', istep1=0,istep2=50000,value1=1,
> value2=4, /
>
> &wt type='TORSION', istep1=0,istep2=50000,value1=1,
> value2=4, /
>
> &wt type='END' /
> LISTOUT=POUT
> DISANG=./REFINE.RST
> DIPOLE=./1.anneal/DIPOLE.RST
>
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>
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Received on Thu Feb 25 2010 - 14:00:02 PST
