Huh!!
Your script is wrong during minimisation. Use these scripts for
minimisation. Once you into MD step after some initial velocity if you put
irest=0, and ig=-1 and tempi and temp0 equal to 300K then it will assign
initial velocities based on boltzman weighed.
Attach herewith all the inputs that might help you
Partial_Mini.in
Initial minimization of MMP3 (MMMM): solvent molecules and added ions
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 750,
ntb = 1,
ntr = 1,
cut = 12.0,
/
Hold the Protein fixed
10.0
RES 1 557
END
END
Full_Mini.in
full minimization of MMP3 (MMMM): protein, ligand, solvent molecules and
added ions
&cntrl
imin = 1,
maxcyc = 200,
ncyc = 50,
ntb = 1,
ntr = 0,
cut = 12.0,
Drms = 0.0001,
/
END
Heating.in
Heating Step of MMP3 (MMMM): stage-5
&cntrl
imin= 0,
irest=1,
NTX=1,
ntb= 1,
NTPR=500,
NTWX=500,
NTWR=500,
ntr=1,
Tempi=0.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut= 12.0,
nstlim=2500,
dt=0.002,
/
Keep Protein and inhibitor fixed with weak restraints
10.0
RES 1 557
END
END
equil.in
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=1,
NTX=7,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
ntr=0,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=250000,
dt=0.002
/
md.in
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=0,
ig=-1
NTX=7,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
ntr=0,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=2500000,
dt=0.002
/
On Tue, May 20, 2014 at 6:39 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Minimization does not use velocity information, only MD (which is why
> you don't have velocity info in your restart to begin with), so you
> don't need to set 'irest' if you are continuing a minimization.
>
> -Dan
>
> On Tue, May 20, 2014 at 10:14 AM, Valentina Romano
> <valentina.romano.unibas.ch> wrote:
> > Dear users
> >
> > I ran a min. step for 2500 steps.
> > Since the energy was not stable and the RMS still high i decided to run
> a second min. (2500 additional steps) using as starting point the files i
> got from the previous step.
> >
> > In the first step:
> > -r PknGAde-min.rst and -ref PknGAde-solv-min.rst
> >
> > The 2nd step input file was the following:
> >
> > Initial XMIN minimisation of PknG-Adenine complex: complex, water and
> ions
> > &cntrl
> > imin=1,
> > maxcyc=2500,
> > ntmin=3,
> > irest=1,
> > ntx=5,
> > ntb=1,
> > igb=0,
> > ntr=0,
> > cut=10,
> > ntpr=10, ntwx=10, ntwr=1000
> >
> > And i ran sander as follow:
> > sander -O -i PknGAde-min.in -o PknGAde-min.out -p
> ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde-min.rst -r
> PknGAde-min.rst -ref PknGAde-solv-min.rst -x PknGAde-min.mdcrd &
> >
> > Thus I used as coord. the file I got from the previuos min.
> >
> > I got the following error:
> > ERROR: I could not find enough velocities in
> > PknGAde-min.rst
> >
> > I do not understand why i got that error.
> > Anyone can help me in understanding what happened?
> >
> > Thank you
> > Valentina
> >
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
> Swiss Institute of Bioinformatics
> > Klingelbergstrasse 61 | CH-4056 Basel |
> >
> > Phone: +41 61 267 15 80
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed May 21 2014 - 00:30:02 PDT
