From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Thu Oct 18 2007 - 00:51:36 CDT
Hi Everyone,
I am trying to do an mcti pmf calculation. I am using .parm7 file
generated by xleap/amber9/rna.ff99.
From the previous posts I learned that the default segname that should
be used is "MAIN" (for restraints the atoms are to be specified
[segname,resid, atomname]).
However I still get a parsing error for my selection (see below).
Thanks in advance to anyone that can help with an advice,
George Giambasu
input:
------------------------------------------------------------------------------
freeenergy on
freeEnergyConfig {
urestraint {
dihe pmf (MAIN, 0, C4') (MAIN, 1, P) (MAIN, 1, C4') (MAIN, 2, P)
kf=20.0, low=164.0, hi=220
}
mcti {
task = stepup
equiltime = 10 ps
accumtime = 10 ps
numsteps = 5
print = 1 ps
}
mcti {
task = stepdown
}
}
--------------------------------------------------------------------------------
Here is the output:
Info: FREE ENERGY PERTURBATION CONFIG
Info: ***********************************
urestraint {
dihe pmf (MAIN, 0, C4') (MAIN, 1, P) (MAIN, 1, C4') (MAIN, 2, P)
kf=20.0, low=164.0, hi=220
}
mcti {
task = stepup
equiltime = 10 ps
accumtime = 10 ps
numsteps = 5
print = 1 ps
}
mcti {
task = stepdown
}
Info: ***********************************
FreeEnergy:
FreeEnergy: Problem parsing input parameters
FreeEnergy: Error: Invalid AtomID
FreeEnergy: Read Until: (main, 0, c4') (main, 1, p) (main, 1, c4')
(main, 2, p) kf=20.0, low=164.0, hi=220
}
mcti {
task = stepup
equiltime = 10 ps
accumtime = 10 ps
numsteps = 5
print = 1 ps
}
mcti {
task = stepdown
}
FreeEnergy:
FATAL ERROR: FreeEnergy: Fatal Parsing Error
Stack Traceback:
[0] _Z7AddAtomR6AGroupPcS1_R22GlobalMasterFreeEnergy+0x2b4 [0x8229eac]
[1] _Z8AddAtomsR6AGroupPcR22GlobalMasterFreeEnergy+0x4d6 [0x8228fb2]
[2] _Z12GetRestraintPcRiR22GlobalMasterFreeEnergy+0x102 [0x8226796]
[3]
_Z14ReadRestraintsPcR17ARestraintManagerR22GlobalMasterFreeEnergy+0x68
[0x822a200]
[4]
_Z9ReadInputPcR17ARestraintManagerR14ALambdaManagerR22GlobalMasterFreeEnergyd+0x166
[0x822a436]
[5] _ZN22GlobalMasterFreeEnergy15user_initializeEv+0x12a [0x823feae]
[6] _ZN22GlobalMasterFreeEnergy10initializeEv+0x132 [0x824007a]
[7] _ZN22GlobalMasterFreeEnergyC9Ev+0x67 [0x823ef3f]
[8] _ZN22GlobalMasterFreeEnergyC1Ev+0xb [0x823efb7]
[9] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x425 [0x8118de9]
[10] _ZN4Node7startupEv+0x13e [0x827d052]
[11] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x13 [0x827cf0b]
[12] CkDeliverMessageFree+0x29 [0x8322f7d]
[13] _Z15_processHandlerPvP11CkCoreState+0x417 [0x83225bf]
[14] CmiHandleMessage+0x1d [0x837c885]
[15] _ZN9ScriptTcl9initcheckEv+0x7f [0x82b9faf]
[16] _ZN9ScriptTcl3runEPc+0xaa [0x82b6b16]
[17] main+0x1d6 [0x80df19a]
[18] __libc_start_main+0xdc [0xb7cefebc]
[19] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59
[0x80dba71]
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:23 CST