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
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AMBER mailing list
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Received on Mon Jun 21 2010 - 08:30:04 PDT
