Hello Amber users
I am using Amber 9 , I want to apply TMD on a inhibitor docked to my
protein. While running the TMD I am getting the following error"
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 1620 3196 3197
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Generally to recver from this problem reduction in the force constant ot
time step is the good idea
but here IN TMD I am not all using any restraints so what else is the reason
for this.
My input file :
&cntrl
imin = 0, ntx = 7, irest = 1,
ntpr = 100, ntwx = 500, ntwe = 0,
ntc = 2, ntf = 2,
nstlim = 250000, dt = 0.002,
tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
ntb = 1, ntp = 0,cut=10.0,iwrap=1,ntr=0,
itgtmd=1,tgtrmsd=11.11, tgtmdfrc=5.0, tgtrmsmask=":321",tgtfitmask=":
1-320.CA,C,N"
&end
&wt type='TGTRMSD', istep1 =0,istep2 = 50000,value1 = 11.11,
value2 = 5.55, &end
&wt type='TGTRMSD', istep1 =50001, istep2 = 250000,value1 = 5.55,
value2 = 0.0, &end
&wt type="END" &end
here I am using such a high value of RMSD I dont know whether it is
fissible or not. Suggest something.
Thanks & Regards
Gurpreet
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Received on Sun Oct 21 2007 - 06:07:12 PDT
