atom specification in smd/tclforces for amber topology/parameter based systems

From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Mon Mar 07 2005 - 14:50:20 CST

Hi all,
Since, amber parameter/structure files don't carry info on segment ids, is
there another way to specify the pulled atoms in the tclforces script file in
an smd simulution?. I already tried including a psf file built with vmd for
this but was unable to start the simulation.

here is my namd output

-----
Info: Entering startup phase 6 with 10735 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 10736 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 705 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 5.55865e-22 (656)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 5.04871e-29 (651) 1.00974e-27
(633)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 8.47033e-22 (693) 1.48231e-21
(697)
TCL: atom not found
FATAL ERROR: atom not found
    while executing
"atomid BH 2 H4"
    invoked from within
"set id1 [atomid BH 2 H4]"
    (file "smd.tcl" line 3)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: atom not found
    while executing
"atomid BH 2 H4"
    invoked from within
"set id1 [atomid BH 2 H4]"
    (file "smd.tcl" line 3)

Stack Traceback:
  [0] CmiAbort+0x48 [0x63c26f]
  [1] _Z8NAMD_diePKc+0x46 [0x4907c6]
  [2] _ZN15GlobalMasterTcl10initializeEv+0x36a [0x554dfa]
  [3] _ZN15GlobalMasterTclC1Ev+0x43 [0x553fb3]
  [4] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x266 [0x4b49b6]
  [5] _ZN4Node7startupEv+0x2f0 [0x5890a0]
  [6] CkDeliverMessageFree+0x39 [0x605553]
  [7] _Z15_processHandlerPvP11CkCoreState+0x2c5 [0x606559]
  [8] CmiHandleMessage+0x28 [0x640bc4]
  [9] CsdScheduleForever+0x52 [0x640cf3]
  [10] CsdScheduler+0xd [0x640c83]
  [11] _ZN9ScriptTcl11Tcl_measureEPvP10Tcl_InterpiPPc+0x11a [0x5b473a]
  [12] TclInvokeStringCommand+0x91 [0x653658]
  [13] TclExecuteByteCode+0x856 [0x66df3f]
  [14] Tcl_EvalObjEx+0x2bb [0x65406b]
  [15] Tcl_WhileObjCmd+0x6a [0x6607ed]
  [16] namd2 [0x6894a8]
  [17] Tcl_EvalEx+0x176 [0x689aeb]
  [18] Tcl_EvalFile+0x134 [0x6814f4]
  [19] _ZN9ScriptTcl3runEPc+0x12 [0x5b6022]
  [20] main+0x1d6 [0x493016]
  [21] __libc_start_main+0xa0 [0x2a95d0e0e0]
  [22] cos+0x1ca [0x4900ea]
Charm++ fatal error:
FATAL ERROR: atom not found
    while executing
"atomid BH 2 H4"
    invoked from within
"set id1 [atomid BH 2 H4]"
    (file "smd.tcl" line 3)

Aborted

-- 
Jerry Ebalunode
RM 402F Houston Science Center
Dept. of Biology and Biochemistry
University of Houston
4800 Calhoun Road
Houston, TX 77204
"No trees were killed in the posting of this message. However a large number 
of electrons were terribly inconvenienced..." 
Marcos Topete

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