AMBER Archive (2007)

Subject: Re: AMBER: Reg restraint value obtained during umbrella sampling

From: D.Usharani (usha_at_ipc.iisc.ernet.in)
Date: Thu May 31 2007 - 13:28:50 CDT

Dear amber users,

Thank you for your quick reply, my out put file has given the lines
mentioned by you and they are as follows:
**************
           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 DUMPFREQ 10 0 0.000000 0.000000 0 0
                         ** No weight changes given **

 RESTRAINTS:
 Requested file redirections:
  DISANG = distcom112.RST
  DUMPAVE = umbcom.112
 Restraints will be read from file: distcom112.RST
 Here are comments from the DISANG input file:

                       Number of restraints read = 1

                  Done reading weight changes/NMR restraints
********************
so from this it is understood there is one restrain considered, but
throughout the simulation run there is no restraint value.

I am interested in doing this as i want to do the PMF calculation using
umbrella sampling. The restrain value obtained is further used for WHAM to
generate the PMF. So the restraint values are important for the further
analysis.

Thanks in advance
usha

> Hello,
> It's difficult to see any error in the input file pasted on a mailer...
> Check your output file, it should give you more informations on your
> input.
> You should see something like this in the mdout:
> **********************
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> DISAVI 0 1 14.500000 0.000000 0 0
> ** No weight changes given **
>
> RESTRAINTS:
> Requested file redirections:
> LISTOUT = POUT
> DUMPAVE = DUMP
> DISANG = RST.F
> Restraints will be read from file: RST.F
> Here are comments from the DISANG input file:
> #EQUILIBRATE ***********
>
>
> Number of restraints read = 12
>
> Done reading weight changes/NMR restraints
> ********************
>
>
> If it is the case, amber has understood that you have some restraints
> defined.
> If not, check your input again.
>
> Also, I suggest you to think about what your want to obtain with your
> umbrella
> sampling. I'm not sure that you can get relevant structural inforation
> about the
> association of two DNA strands from such calculation.
> The number of degrees of freedom is tremendously large and your simulation
> won't
> probably sample the proper Boltzman-weighted structures in each US window,
> unless you intend to perform millisecond scale MD !!...
>
> Good luck
> Jerome
>
>
> Selon "D.Usharani" <usha_at_ipc.iisc.ernet.in>:
>
>>
>>
>> Dear amber users,
>>
>> I am a new subscriber for amber. I am trying to do an umbrella sampling
>> for a 12 base pairs two DNAs separated by certain distance using amber8.
>> The reaction coordinate is along the two center of mass of DNA. The
>> distance restraint file I used is according to amber8 manual (pg 173)
>> and
>> is as follows:
>> &rst
>> iat= -1,-1, nstep1=1, nstep2=6000,
>> iresid=1,irstyp=0,ifvari=1,ninc=0,imulti=0,ir6=0,ifntyp=0,
>> r1=0.00000E+00, r2=112.0000, r3=112.0000, r4=99.0000,
>> rk2=5.0000, rk3=5.0000,
>> r1a=0.00000E+00, r2a=110.0000, r3=110.0000, r4=99.0000,
>> rk2a=5.0000, rk3a=5.0000,
>> igr1 = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
>> 19, 20, 21, 22, 23, 24, 0,
>> grnam1(1) ='P', grnam1(2)= 'P', grnam1(3)='P', grnam1(4)='P',
>> grnam1(5)='P', grnam1(6)='P', grnam1(7)='P', grnam1(8)='P',
>> grnam1(9)='P', grnam1(10)='P', grnam1(11)='P', grnam1(12)='P',
>> grnam1(13)='P', grnam1(14)='P', grnam1(15)='P', grnam1(16)='P',
>> grnam1(17)='P', grnam1(18)='P', grnam1(19)='P', grnam1(20)='P',
>> grnam1(21)='P', grnam1(22)='P', grnam1(23)='P', grnam1(24)='P',
>> igr2 =
>> 25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,0,
>> grnam2(1) ='P', grnam2(2)= 'P', grnam2(3)='P', grnam2(4)='P',
>> grnam2(5)='P', grnam2(6)='P', grnam2(7)='P', grnam2(8)='P',
>> grnam2(9)='P', grnam2(10)='P', grnam2(11)='P', grnam2(12)='P',
>> grnam2(13)='P', grnam2(14)='P', grnam2(15)='P', grnam2(16)='P',
>> grnam2(17)='P', grnam2(18)='P', grnam2(19)='P', grnam2(20)='P',
>> grnam2(21)='P', grnam2(22)='P', grnam2(23)='P', grnam2(24)='P',
>> /
>>
>> my sander input file is :
>> &cntrl
>> nmropt = 1,
>> ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
>> ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
>> ntwprt = 0, ntwr = 500,
>>
>> ntf = 2, ntb = 1, dielc = 1.0,
>> cut = 9.0, nsnb = 10,
>> scnb = 2.0, scee = 1.2,
>>
>> ipol = 0,
>>
>> ibelly = 0,
>>
>> imin = 0,
>> nstlim = 100000,
>> nscm = 1000,
>> t = 0.0, dt = 0.001,
>>
>> temp0 = 300.0, tempi = 300.0,
>> ig = 71277,
>> ntt = 1,
>> tautp = 1.0,
>> vlimit = 20.0,
>> ntp = 0, pres0 = 1.0, comp = 44.6,
>> taup = 0.5,
>> ntc = 2, tol = 0.0005,
>>
>> /
>> &ewald
>> /
>> &wt type='DUMPFREQ', istep1=10 /
>> &wt type='END' /
>> DISANG= distcom112.RST
>> DUMPAVE=umbcom.112
>>
>> The output file and trajectory files didn't have any errors written, but
>> the umbcom.112 file that has been generated during the run should have
>> restraint value of distance which was not printed, instead it is like
>> this
>>
>> Restraints on step 0:
>> 0.000
>> Restraints on step 10:
>> 0.000
>>
>> Even with varying the force constant (rk2, rk3 ) values of 5-25kcal/mol
>> also it didn't print any value.
>>
>> Can any one tell me where is the mistake? Is that i cant define the
>> residue in the center of mass restraint? If so how should be the input
>> distance restraint file for umbrella sampling?
>>
>>
>>
>> Thanks in Advance
>>
>> usha
>> Inorganic and physical chemistry
>> Indian Institute of Science
>> Bangalore -12
>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>
>
> --
> Jérôme Golebiowski, Ph D.
> Lab CMBA, University of Nice Sophia Antipolis
> 06108 nice cedex 2
> France
> tel: +33 (0)4 92 07 61 03
> http://www.unice.fr/lcmba
> http://www.unice.fr/lcmba/golebiowski
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>

*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
D.Usharani
c/o Prof E.D.Jemmis
Inorganic and PhysicalChemistry
Indian Institute of Science
Bangalore -560012
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu