Thanks for reply
Yes during installtion I have already fixed. Bugfix file (bugfix.all,
apply_bugfix_all.x)
for Amber10 was downloded from amber website.
> 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
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Jun 21 2010 - 09:30:05 PDT
