Dear Amber users/developers,
I need to increase the distance between two atoms under constant velocity
and constant force regime. It seems that I must change the values of r4 and
r4a in the restraint file depending on the final value of the SMD distance
(r2a) to obtain a parabolic or linear restraint potential. I set these
parameters to my desired values in the restraint file, but the output file
shows that my desired values are ignored by the code and changed to what
the code prefers. Here is an example of my restraint file and its output:
RST file: ------------------------------------------------------------------
# SMD under constant velocity
&rst iat=379,761, ifvari=1, nstep1=0, nstep2=0, r1=0.0, r2=86.979,
r3=86.979, r4=386.979, r1a=125.997, r2a=220.979, r3a=220.979, r4a=486.979,
rk2=0.125, rk3=0.125, rk2a=0.125, rk3a=0.125, /
Output: ------------------------------------------------------------------
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
DUMPFREQ 500 0 0.000000 0.000000 0 0
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = dist.RST
DUMPAVE = F_vs_d
LISTIN = POUT
LISTOUT = POUT
Restraints will be read from file: dist1.RST
Here are comments from the DISANG input file:
jar option running
******
O3' ( 379)-DH ( 761) NSTEP1= 0 NSTEP2=******
R1 = -13.021 R2 = 86.979 R3 = 86.979 R4 = 186.979 RK2 = 0.125 RK3 = 0.125
R1A= 120.979 R2A= 220.979 R3A= 220.979 R4A= 320.979 RK2A= 0.125 RK3A= 0.125
Rcurr: 86.979 Rcurr-(R2+R3)/2: 0.000 MIN(Rcurr-R2,Rcurr-R3): 0.000
Number of restraints read = 1
Done reading weight changes/NMR restraints
------------------------------------------------------------------
I use Amber12 with all patches applied. Is there a mistake in my input file
or it is a bug?
I'd be so grateful if anyone could help me on these issues.
Best regards, AMNN
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Received on Sun Feb 23 2014 - 00:30:02 PST
