It does appear only the backbone atoms are being chosen. Did you apply all
bugfixes and recompile? You should also consider the tip regarding setting
ntwx=1 and seeing where it blows up.
Good luck!
Jason
On Mon, Jun 21, 2010 at 11:10 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> But when I am using
>
> Hold only backbone atom fixed
> 500.0
> FIND
> * * M *
> SEARCH
> RES 1 129
> END
> END
>
> It is giving the folowing output:
>
> ----- READING GROUP 1; TITLE:
> Hold only backbone atom fixed
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
> ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED
> IN
> GROUP BELOW
>
> GRAPH NAME = * SYMBOL = * TREE SYMBOL = M RESIDUE TYPE
> = *
>
> GRP 1 RES 1 TO 129
> Number of atoms in this group = 381
> ----- END OF GROUP READ -----
>
> My protein have only 2005 atoms number of atoms seleted is only 381 so
> I think it is selecting only backbone atoms as according to manual.
>
> >
> >
> > Hello,
> >
> > Set ntwx to 1 and try to visualize what's happening to your system to
> make
> > it blow apart. Secondly, I would leave tol at its default value.
> Finally,
> > the restraints that you're applying appear to be applied to every atom in
> > the system, not just the backbone. To restrain the backbone, you can use
> > "restraintmask=".CA,N,C,O" and restraint_wt to set the strength of the
> > restraints. You'll have to get rid of the restraint cards at the bottom
> of
> > your input file, though. I would also leave vlimit at its default value.
> > Why are you changing it?
> >
> > All the best,
> > Jason
> >
> > On Mon, Jun 21, 2010 at 7:10 AM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >>
> >> Hello all
> >>
> >> I am doing constant pH simulation using Amber10.
> >> For this
> >> 1) I have minimize protein:
> >> a)using restraint on backbone with force constant 500.0
> >> b)whole sytem with restraint
> >>
> >> 2)Heating of system for 300ps with temperature increment 1K/1ps,during
> >> heating
> >> here i have used tol=.00001 though in manual for constant pH
> simulation
> >> it
> >> is tol=.000001. Actualy I have done it by mistake.Here I restraint
> backbone
> >> with
> >> foce constant 10.0 .
> >>
> >> Here is my input file:
> >> imin=0,
> >> irest=0,ntx=1,ntb=0,cut=30,
> >> ntpr=200,ntwx=200,ntwr=500,
> >> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> >> nstlim=150000,dt=.002,ntr=1,
> >> ntt=1,tempi=0,temp0=300,nmropt=1,
> >> scee=1.2,saltcon=0.1,tol=0.00001,vlimit=15,
> >> icnstph=1,solvph=4,ntcnstph=5
> >> &end
> >> &wt
> >> type='TEMP0', istep1=0, istep2=10000, value1=0, value2=20,
> >> &end
> >> &wt
> >> type='TEMP0', istep1=10001, istep2=20000, value1=20, value2=40,
> >> &end
> >> &wt ...........
> >>
> >> type='END'
> >> /
> >> Hold only backbone atom fixed
> >> 10.0
> >> FIND
> >> * * M *
> >> SEARCH
> >> RES 1 129
> >> END
> >> END
> >>
> >>
> >>
> >> 3)Equilibration for 300ps using restraint on backbone with force
> constant
> >> 1.0
> >> this time I use tol=.000001 then I got following error:
> >>
> >> vlimit exceeded for step 78066; vmax = 321.8661
> >> vlimit exceeded for step 78067; vmax = 24.5430
> >> vlimit exceeded for step 78082; vmax = 399.2392
> >>
> >> Coordinate resetting (SHAKE) cannot be accomplished,
> >> deviation is too large
> >> NITER, NIT, LL, I and J are : 0 5 2 19 21
> >>
> >> Note: This is usually a symptom of some deeper
> >> problem with the energetics of the system.
> >>
> >> But when I chage it to tol=.00001 it run upto 300ps
> >>
> >>
> >> 4)In production run again I have use tol=.00001 it stop with following
> >> error :
> >>
> >> vlimit exceeded for step 262668; vmax = 111.4422
> >> vlimit exceeded for step 262669; vmax = 25.1137
> >> vlimit exceeded for step 262699; vmax = 1960.5580
> >>
> >> Coordinate resetting (SHAKE) cannot be accomplished,
> >> deviation is too large
> >> NITER, NIT, LL, I and J are : 0 2 2 19 21
> >>
> >> Note: This is usually a symptom of some deeper
> >> problem with the energetics of the system.
> >>
> >>
> >> Here is the input file:
> >> imin=0,
> >> irest=1,ntx=7,ntb=0,cut=30,
> >> ntpr=200,ntwx=200,ntwr=500,
> >> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> >> nstlim=150000,dt=.002,
> >> ntt=1,tempi=300,temp0=300,
> >> scee=1.2,saltcon=0.1,tol=0.00001,vlimit=15,
> >> icnstph=1,solvph=4,ntcnstph=5
> >> /
> >>
> >>
> >> Where is the problem I am not getting so can anybody suggest me
> >>
> >> With regard
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 21 2010 - 09:30:03 PDT
