AMBER Archive (2007)

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

From: D.Usharani (usha_at_ipc.iisc.ernet.in)
Date: Sat Jun 02 2007 - 06:07:43 CDT

Dear David sir,

I tried four possibilities they are

 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,
           ^^^^^^^^ *******
   r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
      rk2=1.0000, rk3=1.0000,
/

########## then the output is
WEIGHT CHANGES:
 DUMPFREQ 10 0 0.000000 0.000000 0 0
                         ** No weight changes given **
      RESTRAINTS:
 Requested file redirections:
  LISTIN = POUT
  DISANG = distatom.RST
  DUMPAVE = umbdistatompmemd.20
 Restraints will be read from file: distatom.RST
 Here are comments from the DISANG input file:

******
 CA ( 3)-CA ( 14) NSTEP1= 0 NSTEP2=
   0
R1 = 21.281 R2 = 41.281 R3 = 41.281 R4 = 120.281 RK2 = 1.000 RK3 =
1.000
 Rcurr: 21.281 Rcurr-(R2+R3)/2: 20.000 MIN(Rcurr-R2,Rcurr-R3): 20.000
                       Number of restraints read = 1

                  Done reading weight changes/NMR restraints
#############

It has also DUMPAVE value ranging from 21.2-41.8 angstroms.

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 .

In the two results it seems the restraint is like a well with square
bottom parabolic sides.
 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?
****
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,
                                     ^^^^^^
    r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
       rk2=1.0000, rk3=1.0000,
    igr1 = 1,0,
   grnam1 (1) ='CA',
    igr2 = 2,0,
   grnam2 (1) ='CA',

 /

##output 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 = distcom0.RST
  DUMPAVE = umbdistcom0.20
 Restraints will be read from file: distcom0.RST
 Here are comments from the DISANG input file:

 Error: No atom in residue 1
###
i checked the PDB file there is residue 1, by typing mistake of imulti = 1
it didn't gave null values earlier, I tried all key words but couldn't
trace out what went wrong. This felt may not be a bug, but error in the
syntax.

Could you please tell me what is the error in the input file? as for my
biomolecule it is needed.

 I am attaching even the sander input file used for all these runs.

Thanks in advance.
usha
IISc
bangalore


  • application/octet-stream attachment: umb.in

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