On Mon, Jun 27, 2016 at 10:06 AM, bharat gupta <bharat.85.monu.gmail.com>
wrote:
> Hi,
>
> Thank you for again for your advice.
>
>
>> First: if you reply to a digest mail (that contains lots of messages),
>> please
>> delete all the non-relevant material. Otherwise, it is very hard to even
>> find your question.
>>
>
> Sorry for that, I will take care of that while posting the queries again.
>
>>
>> > > > Coordinate resetting (SHAKE) cannot be accomplished,
>> > > > deviation is too large
>> > > > NITER, NIT, LL, I and J are : 0 2 392 803
>> 804
>> > >
>> > > The problem is at atoms 803 and 804. Check your structure carefully
>> at
>> > > that point.
>> > >
>> >
>> > Thank you for your response. I looked at the pdb file and atoms 803 and
>> 804
>> > are O and H, respectively of a water molecule.
>>
>> So: did you "check the structure carefully" in that region? Is there
>> anything
>> special about that water? Have you visualized its interactions with the
>> rest
>> of your system?
>>
> Yes, I checked and I found that the O (803) and H (804) are bonded to one
> of the protein residues. I also checked the density.rst structure in tleap
> using the check command and I found the same problem with three other water
> molecules (which were not shown as an error while performing
> equilibration).
> > check com
> Checking 'com'....
> Warning: Close contact of 1.490077 angstroms between .R<WAT 2455>.A<H1 2>
> and .R<WAT 2470>.A<O 1>
> Warning: Close contact of 1.466524 angstroms between .R<WAT 16301>.A<H1 2>
> and .R<WAT 17044>.A<O 1>
> Warning: Close contact of 1.442608 angstroms between .R<WAT 16436>.A<H2 3>
> and .R<WAT 16652>.A<H2 3>
> Checking parameters for unit 'com'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 3
> Unit is OK.
>
> So what could be the problem? Am I not minimizing the solute enough. My
> current settings are:
>
> Minimization of waters
> &cntrl
> imin=1, maxcyc=10000, (*in tutorial maxcyc was 5000*)
> ncyc=5000, ntb=1, (*in tutorial ncyc was 3000*)
> cut=12, ntpr=5,
> ntr=1,
> restraint_wt=2.0
> &end
> Group input for restrained atoms
> 100.0
> RES 1 535
> END
> END
>
> I changed the values for maxcyc and ncyc in my settings and rest
> parameters were same.
>
> Or the box size might be small?? I used 12.0 and closeness 0.78, as
> mentioned in the tutorial.
>
>
>
> Regards
> BM
>
>
I also checked the system after minimization of the entire system without
restraints and there were no close contacts (using tleap and check
command). The problems arises after heating. I even tried heating for a
large number of steps, but that didn't solve the problem either..
I would be happy to seek your advice in this regard.
Thanks
BM
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Received on Mon Jun 27 2016 - 06:30:03 PDT
