Waouh.
Thanks!
I'm kind of ashamed for having such a bad structure. There was many
sidechains missing in the original Xray file and I guess that tleap
didn't add them correctly. Usually a simple minimization gives a good
starting point. That was not the case here I suppose.
I look forward to being able to use that sanity check before running MDs
in the future.
Thanks again!
Gerald.
On 07/15/2016 11:53 PM, David Cerutti wrote:
> Let me shamelessly plug my new toy in mdgx: configuration sampling, to be
> released in AmberTools v17 after I do a bit more polishing. I'm not using
> it for its primary purpose, but it does perform energy minimizations with
> array of NMR restraints and thereafter creates a report file containing
> information to help identify bad conformations and help the user to see "I
> guess it doesn't bend that way!" For this case, I am making use of the
> sanity checking. Here's the output:
>
> <++>-----------------------------------------------------------------------<++>
> (3.) Basic sanity checks. If a configuration fails these tests, it was not
> printed out for further consideration but the reasons it failed will be
> summarized here. The tests are that, first, no bond of a configuration
> may be strained more than 10.00 kcal/mol. Furthermore, no angle may be
> strained more than 10.00 kcal/mol. Finally, the maximum tolerated
> restraint energy (summed over all restraints) is 200.00 kcal/mol. If
> any
> of these tests seem too stringent or not tight enough, the thresholds
> may
> be changed in the &configs namelist.
>
> - Configurations passing all sanity checks: 0
> - Configurations failing bond sanity check: 1
> - Configurations failing angle sanity check: 1
> - Configurations failing restraint sanity check: 0
>
> Descriptions of each problematic configuration follow, along with the
> names and numbers of atoms involved in each feature creating the problem.
> - Configuration 1:
> Strain is 478.9827 for bond NE -CZ (208, 210)
> Strain is 34.6589 for angle NH1 -CZ -NH2 (211, 210, 214)
> Restraint binding atoms () strained to 0.0000
> <++>-----------------------------------------------------------------------<++>
>
> Look at atoms 208 and 210 in Arg12, I see that, yes, it's stabbed right
> through a nearby Phenylalanine.
>
> Dave
>
>
> On Fri, Jul 15, 2016 at 5:18 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Gerald.
>>
>> If you share your files we can take a look on my group's side.
>>
>> We have seen this before due to a VERY weird issue. There are cases
>> where tleap decides to create carbon chains going through the middle of
>> a phenyl ring for instance. Incredibly enough, some of these are
>> perfectly stable at 2 fs, even though they are wrong. 4 fs forces the
>> issues and things blow up, but it has nothing to do with the time step,
>> it is tleap's fault. I suggest you rerun with 4 fs and ntwx=1, and look
>> at your trajectory to see what blows up.
>>
>>
>> Adrian
>>
>>
>>
>> On 7/15/16 5:14 PM, Gerald Monard wrote:
>>> Hello,
>>>
>>> On 07/15/2016 09:56 PM, Hai Nguyen wrote:
>>>> quick question: have you used ParmEd to change the mass yet?
>>>>
>>> Yes. I forgot to say: I've modified the topology file with the
>>> HMassRepartition command in parmed and I have tested both the "normal"
>>> repartioning and the "dowater" option. Same results.
>>>
>>> Gerald.
>>>
>>>> Hai
>>>>
>>>> On Fri, Jul 15, 2016 at 3:54 PM, Gerald Monard <
>>>> Gerald.Monard.univ-lorraine.fr> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I have a protein system in water (321,300 atoms including ~100,000
>> water
>>>>> molecules). I'm trying to use Hydrogen Mass Repartitioning (HMR) to
>>>>> benefit a 4 fs timestep. However, it seems to fail. dt = 0.002 is OK,
>>>>> but with dt = 0.003, the temperature goes bad after a few thousands
>>>>> steps, and with dt = 0.004, it's even faster. This is for pmemd.cuda
>>>>> with Amber16 (all last patches applied) as well as pmemd.MPI.
>>>>>
>>>>> The mdin file is:
>>>>> &cntrl
>>>>> imin = 0, ntx = 5, irest = 1,
>>>>> dt = 0.004, nstlim = 1000000,
>>>>> ntb = 1,
>>>>> ntt = 1, ig = -1, temp0 = 300.,
>>>>> ntc = 2,
>>>>> ntpr = 1000, ntwx = 10000, ntwv = 00, ntwe = 10000,
>>>>> /
>>>>>
>>>>> From the mdin of the GPU benchmark, I've also tried to add tol =
>>>>> 0.000001 as well as ntf = 2. No improvement.
>>>>>
>>>>> Any idea?
>>>>>
>>>>> Gerald.
>>>>>
>>>>> --
>>>>>
>>>>>
>> ____________________________________________________________________________
>>>>>
>>>>> Prof. Gerald MONARD
>>>>> SRSMC, Université de Lorraine, CNRS
>>>>> Boulevard des Aiguillettes B.P. 70239
>>>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>>>>
>>>>> e-mail : Gerald.Monard.univ-lorraine.fr
>>>>> tel. : +33 (0)383.684.381
>>>>> fax : +33 (0)383.684.371
>>>>> web : http://www.monard.info
>>>>>
>>>>>
>>>>>
>> ____________________________________________________________________________
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
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>>
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
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--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Fri Jul 15 2016 - 15:30:02 PDT
