Daer David Sir,
Thank you very much, It is working by removing the space. Now when i
applied it for the DNA by defining the P atom of each base pair. The
input is as follows:
*********************
&rst
iat= -1,-1, nstep1=1, nstep2=50000,
iresid=0,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
r1=0.00000, r2=112.0000, r3=112.0000, r4=200.0000,
rk2=5.0000, rk3=5.0000,
r1a=0.00000, r2a=110.0000, r3a=110.0000, r4a=200.0000,
rk2a=5.0000, rk3a=5.0000,
igr1 =
12,29,62,92,125,157,189,221,253,283,316,346,391,408,441,471,504,536,568,600,632,662,695,725,0,
grnam1='C6','P','P','P','P','P','P','P','P','P','P','P','C6','P','P','P','P','P','P','P','P','P','P','P',
igr2 =
770,787,820,850,883,915,947,979,1011,1041,1074,1104,1149,1166,1199,1229,1262,1294,1326,1358,1390,1420,1453,1483,0,
grnam2='C6','P','P','P','P','P','P','P','P','P','P','P','C6','P','P','P','P','P','P','P','P','P','P','P',
/
***********
There are two DNA's in the system that are seperated by 112.0 Angstroms
and i defined each DNA as one group. I want to calculate the PMF along
the reaction coordinate moving from 112 to 60 angstroms.
As by giving only phosphorus atom for the COM restriant there is a loss of
base pair stacking along the run. Is there a better way to define the COM
for each DNA? As it is dodecamer DNA it has 758 atoms and number of
aoms that can be defined has 200 as alimit under each group.
I also used iresid=1 and defined the resdiues but it gives the error
MAXGRP=3 exceeded error. So what can i do?
Thanks in advance
usha
> On Sat, Jun 02, 2007, D.Usharani wrote:
>>
>> 1. iresid=0 defining the distance restraint with atoms
>> &rst
>> ixpk =0, nxpk =0 iat = 3, 14,
>> iresid=0,irstyp=1,ifvari=0,ninc=0,imult=1,ir6=0,ifntyp=0,
>> ^^^^^^^^ *******
>
> irstyp = 1 is very rarely used: I would not recommend it unless you are
> sure
> you understand what it is doing.
>
>>
>> 2. Since the R1, R2, R3 and R4 values are not as given n the restraint i
>> reseted irstyp=0 in the above input file.
>>
>> ####then out put is
>> 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:
>> LISTIN = POUT
>> DISANG = distatom0.RST
>> DUMPAVE = umbdistatom0.20
>> Restraints will be read from file: distatom0.RST
>> Here are comments from the DISANG input file:
>>
>> ******
>> CA ( 3)-CA ( 14) NSTEP1= 0
>> NSTEP2=
>> 0
>> R1 = 0.000 R2 = 20.000 R3 = 20.000 R4 = 99.000 RK2 = 1.000 RK3 =
>> 1.000
>> Rcurr: 21.281 Rcurr-(R2+R3)/2: 1.281 MIN(Rcurr-R2,Rcurr-R3):
>> 1.281
>> Number of restraints read = 1
>>
>> Done reading weight changes/NMR restraints
>> ###########
>> So here R1-R4 values are as given in input file and DUMPAVE values are
>> also 21.2- 19.77 .
>
> Is this not what you want?
>
>>
>> In the two results it seems the restraint is like a well with square
>> bottom parabolic sides.
>
> This is correct, except that when r2 = r3 (as in your case) the width
> of the "square bottom" is zero, so you just have a parbola.
>
>> but I want to understand what does this Rcurr values signifies?
>> what does the RESTRAINT printed at each step value signifies? and why
>> does it decreases and becomes zero?
>
> Rcurr is the current value of the distance. RESTRAINT is the restraint
> energy; it decreases because md simulations tend to populate the regions
> of
> lowest energy.
>
>> ****
>> EELEC = -6781.4141 EHBOND = 0.0000 RESTRAINT =
>> 0.2340
>> EAMBER (non-restraint) = -5733.2865
>> Ewald error estimate: 0.4602E-02
>> ------------------------------------------------------------------------------
>>
>> NMR restraints: Bond = 0.234 Angle = 0.000 Torsion =
>> 0.000
>> *******************
>>
>> 3. Now I tried with ifvari=1 and input for 10ps run is
>>
>> &rst
>> ixpk =0, nxpk =0 iat = 3, 14, nstep1=1, nstep2=10000,
>> iresid=0,irstyp=0,ifvari=1,ninc=0,imult=1,ir6=0,ifntyp=0,
>> r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
>> rk2=1.0000, rk3=1.0000,
>> r1a=0.00000, r2a=18.0000, r3a=18.0000, r4a=99.0000,
>> rk2a=1.0000, rk3a=1.0000,
>> /
>> ### output read correctly the input and restraint and the DUMPAVE value
>> is ranging from 20-18.0 gradually through NSTEPS, and the RESTRAINT
>> though decreasing has a value throughout the run of 10ps.
>>
>> 4. By this i understood that simple distance restraint is working but
>> when
>> tried for COM restraint with the below input
>>
>> &rst
>> iat= -1,-1,
>> iresid=1,irstyp=1,ifvari=0,ninc=0,imult=1,ir6=0,ifntyp=0,
>> ^^^^^^
>
> don't set imult=1 unless you really are sure you know what you are doing.
>
>> r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
>> rk2=1.0000, rk3=1.0000,
>> igr1 = 1,0,
>> grnam1 (1) ='CA',
> ^^^^
>
> I don't think you can have a space here.
>
>> I tried all key words
>
> Don't just randomly try changing key words. Spend enough time with simple
> things until you are confident you understand what is going on, then add
> complexity one step at a time.
>
> ...dac
>
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*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
D.Usharani
c/o Prof E.D.Jemmis
Inorganic and PhysicalChemistry
Indian Institute of Science
Bangalore -560012
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
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Received on Sun Jun 10 2007 - 06:07:33 PDT
