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 Wed Feb 22 2017 - 11:00:03 PST
