In my experience, restraint all but hydrogen is not very helpful. (e.g: sidechain overlap).
How is about restraining only the backbone? Or using no restraint in minimization?
Hai
> On Feb 22, 2017, at 9:54 AM, Joseph Salmon <js13559.2013.my.bristol.ac.uk> wrote:
>
> Dear All,
>
>
>
> I have produced .nc files after the heating phase on a large complex. The
> result of loading the file is that all the atoms shoot of in different
> directions (system blows up). The minimisations prior to the heating seem
> to have not worked, with a LINMIN failure reported in the mdout file. An
> example of the minimisation input is:
>
>
>
> Initial minimization of hydrogens
>
> &cntrl
>
> imin=1, maxcyc=5000, ncyc=1000, ntmin=1,
>
> ntpr=1, ntwr=1,
>
> ntb=0, cut=9999.0,
>
> igb=5, rgbmax=15.0,
>
> ntr=1, restraint_wt=25.0, restraintmask='!.H=',
>
> ntxo=1
>
> /
>
>
>
> And heating input:
>
>
>
> Heating system from 0 K to 300 K over 200 ps
>
> &cntrl
>
> imin=0, irest=0, ntx=1,
>
> dt=0.001, ntc=1, ntf=1,
>
> ntb=0, cut=9999.0,
>
> igb=5, rgbmax=15.0,
>
> ntt=3, gamma_ln=2.0, ig=-1,
>
> ntpr=1, ntwx=1, ntwr=100, nstlim=100,
>
> nscm=1000, ioutfm=1,
>
> ntr=1, restraint_wt=5.0, restraintmask='.CA,N,C,O',
>
> ntxo=1,
>
> /
>
> &wt
>
> TYPE='TEMP0', ISTEP1=1, ISTEP2=100000,
>
> VALUE1=0.0, VALUE2=300.0,
>
> /
>
> &wt TYPE='END' /
>
>
>
>
>
> (Please note that here I used ntpr, ntwx and ntwr = 1 to better monitor
> what the problem was)
>
> The complex contains two non-standard ligands which are not covered by the
> standard protein force fields and so on set of parameters were used from a
> previous study and the other were generated using the ff14SB protein and
> GAFF parameters. Simulations have been run on AMBER-16, using CUDA on gpu
> and also on cpu using sander.
>
>
>
> The heating has been attempted without the gradual increase addition also
> with and without a restraint (DISANG file). The minimisation has been
> tested with ncyc = 10, 20, 50, 1000. Changes to the ff14SB have also been
> trialled, for example the ff14SBonlysc, ff12SB. Finally the ligands were
> removed and a minimisation and heating was run on just the protein
> component and this still blew up.
>
>
>
> The LINMIN failure only occurs during the conjugate gradient minimisation.
> During the steepest descent minimisation, there are no error message.
>
> Strangely, during the minimisation, even with ntwr=1, and 1000 steps of
> steepest descent the structure written to the rst7 file is the same as the
> original structure. See the attached mdout file from the minimisation.
>
>
>
> Any help with regards to how to stop it would be greatly appreciated.
> <model_min1.mdout>
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Received on Wed Feb 22 2017 - 09:00:02 PST
