I ran a minimization (2500 steps,restrained solute, and free solvent) till the RMS was lower than before:
NSTEP ENERGY RMS GMAX NAME NUMBER
2500 -1.0766E+05 7.5114E-01 7.8713E+01 C6 3838
Then, i ran a MD (restrained solute, free solvent). The MD stopped at the 2 step:
NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 508.50 PRESS = 0.0
Etot = -69977.4281 EKtot = 29695.7564 EPtot = -99673.1845
BOND = 157.5169 ANGLE = 595.2081 DIHED = 2346.8970
1-4 NB = 824.5288 1-4 EEL = 8930.8544 VDWAALS = 19185.8961
EELEC = -131714.6440 EHBOND = 0.0000 RESTRAINT = 0.5582
EAMBER (non-restraint) = -99673.7427
Ewald error estimate: 0.1422E-03
------------------------------------------------------------------------------
vlimit exceeded for step 2; vmax = 184.6279
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 1924 3839 3846
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
(where 3839 and 3846 are N6 and H62, respectively).
I analyzed the to frames obtained and actually the ligand is much less distorted than before .
The rmds between the 2 frames is 0.147A.
>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?
I used parmchk after running antechember. None parameter was marked as ATTN. I increased the force constants for the improper torsional angles to force the molecule to be planar.
I ran a min of the purine itself.
imin=1,
maxcyc=500,
ntmin=3,
ntb=0,
igb=0,
cut=999.0,
ntpr=1, ntwx=1, ntwr=100
The ligand was still planar.
Then i ran a MD:
1ps MD Adenine
&cntrl
imin=0,
irest=0,
ntx=1,
ig=-1,
ntb=0,
cut=999.0,
ntc=2,
ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,
gamma_ln=5.0,
nstlim=1000, dt=0.001,
ntpr=1, ntwx=1, ntwr=1000
Again the job stopped after 2steps. It was not really distorted and the rmsd was 0.02.
So, I am not understanding why the job stops after 2 steps.
I guess is something related to the parameters i used for the ligand. If yes, how could I solve that 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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>>
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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 Wed May 14 2014 - 07:30:02 PDT
