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.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
>
>
>
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--
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
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Received on Sun Jun 03 2007 - 06:07:27 PDT
