On Tue, May 13, 2014 at 8:30 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1000 -1.0304E+05 4.2733E+00 7.0121E+02 C4 3843
I would consider this RMS gradient to be still pretty high - I usually
minimize until I'm at least in the 10^-1 kcal range.
> I analyzed the 4 frames obtained. At the frame 1, the ligand molecule was completely distorted. And so now the error message makes more sense, since atoms 3834 and 3844 (N9 and H9, respectively) deviated a lot after the 1st MD step.
>
> I am wondering that this behavior is related to the parameters I obtained for the 6 amino purine using Antechamber.
It could be. Assuming you used parmchk2 after running antechamber to
fill in any missing parameters, were there any marked 'ATTN: needs
revision'? Did you try to minimize/run some short MD of the
6-aminopurine by itself to ensure the parameters were sensible?
-Dan
>
> Any suggestions to solve this problem?
>
> Vale
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, May 12, 2014 8:00 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Analysis of minimization stage
>
> Hi,
>
> On Mon, May 12, 2014 at 10:26 AM, Valentina Romano
> <valentina.romano.unibas.ch> wrote:
>> restraintmask=':1-246.CA,C,O,N | .3834-3848',
>
> I don't think this is what you want if atom range 3834-3848 includes
> hydrogen. During minimization you want all of your hydrogen atoms to
> minimize as much as possible. This way during MD when you turn on
> SHAKE (presumably just for bonds to H atoms), all of your X-H bond
> lengths are in a good place. You really only want to restrain your
> heavy atoms initially. Did you check the last few steps of your
> minimization? Does it look flat? What is your RMS gradient? If your
> structure is not well-minimized prior to running any MD you are
> potentially setting yourself up for vlimit errors. Also, have you
> tried using XMIN instead of steepest descent for minimization?
>
> -Dan
>
>
>> ntpr=1, ntwx=1, ntwr=100
>>
>> Atoms from 3834 to 3848 are ligand's atoms (with H atoms).
>>
>> I analyzed the output frames and the ligand was much more stable then before.
>> (The energy was flat and no overlaps were detected).
>>
>> This structure was used as strating point for a short MD (to relax solvent molecules):
>>
>> 15ps MD PknG-Adenine complex: restraints on PknG-Ade residues while the solvent is leeting free
>> to relax
>> &cntrl
>> imin=0,
>> irest=0,
>> ntx=1,
>> ig=-1,
>> ntb=1,
>> ntr=1,
>> cut=10,
>> ntc=2,
>> ntf=2,
>> tempi=300.0,
>> temp0=300.0,
>> ntt=3,
>> gamma_ln=5.0,
>> nstlim=15000, dt=0.001,
>> ntpr=1, ntwx=1, ntwr=1000
>> restraint_wt = 10.0,
>> restraintmask=':1-246.CA,C,O,N | .3834-3848'
>> /
>> Sander stopped again at the begining:
>>
>> vlimit exceeded for step 1; vmax = 82.0601
>>
>> Coordinate resetting (SHAKE) cannot be accomplished,
>> deviation is too large
>> NITER, NIT, LL, I and J are : 0 3 1923 3841 3848
>>
>> Note: This is usually a symptom of some deeper
>> problem with the energetics of the system.
>>
>> If I restrained all ligand's atoms, why atoms 3841 and 3848 are still causing a problem?
>>
>> Analizing the output file i saw a message related to the charge of the whole system:
>>
>> Sum of charges from parm topology file = 0.00099988
>> Forcing neutrality...
>>
>> Could it be a cause of my problem?
>>
>> I ran the MD as:
>>
>> sander -O -i PknGAde-wt-md.in -o PknGAde-wt-md.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde-wt-min.rst -r PknGAde-wt-md.rst -ref PknGAde-wt-min.rst -x PknGAde-wt-md.mdcrd &
>>
>> Thus the set of initial coord and the ref coord are the same (both are the minimized structure), is it correct?
>>
>> Vale
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
>> Klingelbergstrasse 61 | CH-4056 Basel |
>>
>> Phone: +41 61 267 15 80
>>
>>
>> ________________________________________
>> From: Jason Swails [jason.swails.gmail.com]
>> Sent: Monday, May 12, 2014 4:18 PM
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Analysis of minimization stage
>>
>> On Mon, 2014-05-12 at 09:59 -0400, David A Case wrote:
>>> On Mon, May 12, 2014, Valentina Romano wrote:
>>> >
>>> > CPPTRAJ: Trajectory Analysis. V13.22
>>> > ___ ___ ___ ___
>>> > | \/ | \/ | \/ |
>>> > _|_/\_|_/\_|_/\_|_
>>> > AmberParm Title: [default_name]
>>> > Radius Set: modified Bondi radii (mbondi)
>>> > INPUT: Reading Input from file PknGAde-wt-min.check_overlap
>>> > [trajin PknGAde-wt-min.rst]
>>> > [PknGAde-wt-min.rst] contains 1 frames.
>>> > [checkoverlap]
>>>
>>> Try adding the "reportfile overlaps.dat" to the checkoverlap command.
>>> I'm always uncertain about when cpptraj writes things to stdout, and when
>>> they go to one of the data files.
>>
>> Whenever I've used checkoverlaps before the report gets printed to
>> stdout...
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 13 2014 - 09:30:04 PDT
