Dear all,
I am trying to run TGMD for a system: a 124-residue protein in a
waterbox.
Using AMBER7, weighted TGTRMSD from 4.345 to 0, TGTMDMDFRC=10 or 5 or
1, restrain force applied on residue 3-122, job running OK. then I
tried to apply the restraint force on residue 81-86 only, to see if
the structure will go to the reference structure as well. AMBER7 seems
not be able to do this. I move to AMBER8. Here is the input file:
*****************************************************************
#Data collection at 298K
&cntrl
IMIN = 0,ntx=5,irest=1,
ntpr=10, ntwr=500,
ntb=1,ntr=0,
ntf=2,ntc=2,
cut=8.5, nscm = 1000,
NSTLIM = 400000, DT = 0.002,
NTWX=500, NTWV=500,NTWE=500,
TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0,
nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=10.00,
tgtrmsmask=":3-122", tgtfitmask=":81-86 & !.H=",
&end
&wt
TYPE='TGTRMSD', istep1 =0, istep2 = 200000,
value1 = 4.345, value2 = 0.3,
&end
&wt
TYPE='TGTRMSD', istep1 =200001, istep2 = 400000,
value1 = 0.3, value2 = 0.,
&end
&wt
type="END",
&end
&rst
iat(1)=0,
&end
END
***********************************************************************
I got a problem: job stopped immediately, and gave the informatin as
following:
*********************************************
NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 5403.88 PRESS
= 0.0
Etot = 867849.0298 EKtot = 181470.7791 EPtot =
686378.2507
BOND = 1342.9958 ANGLE = 1534.9087 DIHED =
1235.1722
1-4 NB = 1138.3272 1-4 EEL = 5449.3066 VDWAALS =
9292.6310
EELEC = -64101.8524 EHBOND = 0.0000 RESTRAINT =
730486.7616
EAMBER (non-restraint) = -44108.5108
Ewald error estimate: 0.2247E-04
Current RMSD from reference: 13.246
Current target RMSD: 4.345
----------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
0.000
=======================================================================
vlimit exceeded for step 11 ; vmax = 21.4771801052079
vlimit exceeded for step 12 ; vmax = 1952.41027295489
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 439 882 883
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
***********************************************************************
I noticed that the "Current RMSD from reference" is huge different
from the "Current target RMSD". Is my TGTMDFRC too large?? I decreased
this value to 5, then 1, after running several tens steps, jobs
stopped for the same reason too. I read some emails in the mailing
list. the value of TGTMDFRC between 1-5 or 1-10 should be OK. then
does my input file have a problem?
Thank you very much for your help!
Shawn
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 08 2005 - 21:53:00 PDT
