Re: [AMBER] Minimisation error and system blowup for a large protein using implicit solvent

From: Joseph Salmon <js13559.2013.my.bristol.ac.uk>
Date: Wed, 22 Feb 2017 18:37:16 +0000

 Hi,

so when I ran with sander, the first minimisation, with all but H
restrained, had the same REPEATED LINMIN FAILURE, I have attached this. And
the second minimisation with bb restrained aborted due to an error from the
first restart file. Also, the tleap log showed warnings of the type:

** Warning: No sp2 improper torsion term for c1-c2-c1-hc

        atoms are: C3A CAA C2A H4

Also I ran cpptraj and got 5 warnings:

1 Warning: Atoms 3799:MET_199.HB2 and 3806:MET_199.HE1 are close (0.79)

1 Warning: Atoms 5980:TRP_316.CZ2 and 5986:TRP_316.CE3 are close (0.51)

1 Warning: Atoms 5984:TRP_316.CZ3 and 5987:TRP_316.HE3 are close (0.38)

1 Warning: Atoms 29924:PHE_1538.CD1 and 29928:PHE_1538.CZ are close (0.44)

1 Warning: Atoms 29926:PHE_1538.CE1 and 29932:PHE_1538.CD2 are close (0.59)

On Wed, Feb 22, 2017 at 5:12 PM, Nhai <nhai.qn.gmail.com> wrote:

>
>
> Hi
>
> 1. Can you post the min output with CA (or bb) restraint that was run with
> sander?
>
> 2. Have a look a tleap log to see if there is any WARNING
>
> 3. Try to us cpptraj checkstructure to find the overlapping.
>
> Ps: be sure to reply to mailing list.
> Hai
>
> On Feb 22, 2017, at 11:56 AM, Joseph Salmon <js13559.2013.my.bristol.ac.uk>
> wrote:
>
> Hi Hai,
>
> Sorry I should have said, the minimisation has been attempted with
> backbone, just alpha carbon and no restraint. All give REPEATED LINMIN
> FAILURE.
>
> On Wed, Feb 22, 2017 at 4:44 PM, Nhai <nhai.qn.gmail.com> wrote:
>
>>
>> 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>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>


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Received on Wed Feb 22 2017 - 11:00:02 PST
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