Hi,
Thank-you, I was able to run a minimisation with just the BB restrained,
this reduced the LIMIN FAILURE and heating was completed!!
On Wed, Feb 22, 2017 at 6:46 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Hi,
>
> I guess I was not clear. I meant using BB restraint (or even do NOT use
> restraint) in your first minimization (You used to use all but H restraint).
>
> If you look at cpptraj log
>
> >1 Warning: Atoms 5980:TRP_316.CZ2 and 5986:TRP_316.CE3 are close (0.51)
>
> there is strong overlap between two heavy atoms. I guess the point of not
> restraining them is to let them avoid each other.
>
> Also, do you double-check what happens with your structure here?
>
> Hai
>
>
> On Wed, Feb 22, 2017 at 1:37 PM, Joseph Salmon <
> js13559.2013.my.bristol.ac.uk> wrote:
>
>> 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 Thu Feb 23 2017 - 07:30:03 PST
