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
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- application/octet-stream attachment: umb.in
Received on Sun Jun 03 2007 - 06:07:48 PDT
