AMBER Archive (2007)

Subject: Re: AMBER: Potential of mean force, how to calculate rate of dissociation?

From: wang (c00jsw00_at_nchc.org.tw)
Date: Mon May 07 2007 - 01:20:41 CDT

Dear all ,
When I used the SMD module , the moving distance is bigger than 100 A
and the error happened .
Could you tell me how to fix the problem ?
thanks

wang

input
___________________________________________________
&rst iat=1771,3787, r2=63., rk2 = 1000., r2a=300, /
____________________________________________________

error message
____________________________________________________

******
CA ( 1771)-CA ( 3787) NSTEP1= 0 NSTEP2=200000
R1 = -37.000 R2 = 63.000 R3 = 63.000 R4 = 163.000 RK2 =1000.000 RK3 =
1000.000
R1A= -37.000 R2A= 300.000 R3A= 300.000 R4A= 163.000 RK2A= 0.000 RK3A= 0.000
Rcurr: 63.108 Rcurr-(R2+R3)/2: 0.108 MIN(Rcurr-R2,Rcurr-R3): 0.108
ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
Offending re
straint:
******
CA ( 1771)-CA ( 3787) NSTEP1= 0 NSTEP2=200000
R1 = -37.000 R2 = 63.000 R3 = 63.000 R4 = 163.000 RK2 =1000.000 RK3 =
1000.000
R1A= -37.000 R2A= 300.000 R3A= 300.000 R4A= 163.000 RK2A= 0.000 RK3A= 0.00

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