# Re: [AMBER] Problem with rst7

From: Elisa Pieri <elisa.pieri90.gmail.com>
Date: Thu, 25 Aug 2016 13:04:18 +0200

This is what the RESULTS section looks like:

------------------------------------------------------------
--------------------
4. RESULTS
------------------------------------------------------------
--------------------

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 11.96 PRESS =
0.0
Etot = -4871.1063 EKtot = 167.1679 EPtot =
-5038.2742
BOND = 412.9686 ANGLE = 1179.5946 DIHED =
3613.8953
1-4 NB = 2442.1380 1-4 EEL = 17099.2356 VDWAALS =
-896.0282
EELEC = -26098.6669 EGB = -2791.4112 RESTRAINT =
0.0000
-----------------------------------------------------------
-------------------

NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
============================================================
===================

NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = NaN PRESS =
0.0
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 547405.9274 DIHED =
19855.8962
1-4 NB = 0.0000 1-4 EEL = 0.2489 VDWAALS =
0.0000
EELEC = 997.3637 EGB = -66293.8715 RESTRAINT =
289530816.0772
EAMBER (non-restraint) = **************
-----------------------------------------------------------
-------------------

NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
============================================================
===================

NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = NaN PRESS =
0.0
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 638733.4240 DIHED =
19778.0610
1-4 NB = 0.0000 1-4 EEL = 0.2033 VDWAALS =
-0.0000
EELEC = 1464.2886 EGB = -66287.9607 RESTRAINT =
**************
EAMBER (non-restraint) = **************
-----------------------------------------------------------
-------------------

NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
============================================================
===================

NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = NaN PRESS =
0.0
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 763432.0545 DIHED =
19913.0211
1-4 NB = 0.0000 1-4 EEL = 0.3792 VDWAALS =
-0.0009
EELEC = 1296.2820 EGB = -64197.0815 RESTRAINT =
**************
EAMBER (non-restraint) = **************
-----------------------------------------------------------
-------------------

I set such a high restraint weight because I need the protein to be as
freezed as possible, allowing only a cavity to move (as silly as it can
sound). Is there a better way of doing it?

On Thu, Aug 25, 2016 at 11:41 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:

> What do you see in the .out file? You may have to print each step. Look
> for energies going to infinity and note which atom GMAX is on when that
> occurs, then I'd visualize your trajectory to see if there is a specific
> problem in that region. Your restraint weight seems high - you might try
> reducing it to 1 or .1, but I don't have experience with that.
>
> Bill
>
>
> On 8/25/16 2:12 AM, Elisa Pieri wrote:
> > Hi,
> >
> > I heated a protein starting from a good rst7 file using this input:
> >
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntpr=500, ntwx=500, nstlim=1000000,
> > dt=0.002, ntt=3, tempi=10,
> > temp0=300, tautp=2.0, ig=-1,
> > ntp=0, ntc=2, ntf=2, cut=999,
> > ntb=0, igb=2, tol=0.000001,
> > nrespa=1, saltcon=0.1, ntxo=1,
> > gamma_ln=5.0, ntwr=500, ioutfm=1,
> > nmropt=1, ntr=1, restraint_wt=40.0,
> >
> 186-189,191,207,208,211,212,261,265,268,269,272,292,295,296,298',
> > /
> > &wt
> > TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
> > VALUE1=10.0, VALUE2=300.0,
> > /
> > &wt TYPE='END' /
> >
> > The rst7 file that I get at the end is this (first lines):
> > default_name
> > 5649 0.2000000E+04
> > 29.1820225 30.7497409 -22.1838690*******************
> *****************
> > ************************************************************************
> > ************************************************************************
> > ************ 12.7407017************************************************
> > ************************************************ 12.7410547************
> > ************************************************************************
> > ************************************ 94.9745896************ -33.0591310
> > ************************************************************************
> > ************************************************************************
> > 3655.05540903568.3796548 -33.9095279************************************
> > ************************************************************************
> > ************************************************************************
> > ************************************************************************
> > ************5190.95423225142.85060162143.2519731************************
> > 3232.4049918************************************************************
> > ************************************************3535.02488733786.9319069
> > 4008.1078513************************************************************
> > ************************************************************************
> >
> > What happened? Can somebody help me?
> >
> > Thanks!
> > Elisa
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Aug 25 2016 - 04:30:02 PDT
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