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
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Received on Mon May 12 2014 - 11:30:04 PDT
