Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Sep 28 2011 - 15:40:24 CDT

I have a very weird situation; I'm trying to run NAMD2.8 using AMBER forcefields because I anticipate needing to to MMPBSA analyses. In the past, I've never had a problem generating the inputs from pdb files & the AMBER utility tleap. Ever since upgrading to AmberTools1.5 & compiling a parallel version of AMBER11 on the linux station I use for creating the input files, sometimes NAMD can't read the result. The odd thing is that VMD is just fine with it. Here's the last part of my output: Info: Using AMBER format force field!
Info: AMBER PARM FILE 3qasw.prmtop
Info: AMBER COORDINATE FILE 3qasw.inpcrd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (3qasw.prmtop) ...
PARM file in AMBER 7 format
FATAL ERROR: Failed to read AMBER parm file!
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Failed to read AMBER parm file![0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x65 [0x4fb207]
  [0:1] _ZN9NamdState14configListInitEP10ConfigList+0xb77 [0x9607e1]
  [0:2] _ZN9ScriptTcl3runEv+0x151 [0x9e0a3b]
  [0:3] main+0x50d [0x4ff7fd]
  [0:4] __libc_start_main+0xdb [0x3f18c1c3fb]
  [0:5] _ZNSt8ios_base4InitD1Ev+0x3a [0x4fa78a]
Fatal error on PE 0> FATAL ERROR: Failed to read AMBER parm file!TACC: Shutting down parallel environment.
TACC: Shutdown complete. Exiting. Has anyone else seen this, or have any idea what to do? I've already posted a related issue on the AMBER mailer, but no one knew what to do. In that case, I found that although the prmtop file ran with NAMD2.8 & created a trajectory, there was still something wrong because when I tried to do MMPBSA analysis, the routines that separate the structure into protein & ligand crashed with error messages! I thought the prmtop that gave me the above crash was properly formatted because the tool ante-MMPBSA was able to resolve the structure into its dimeric units [I want to be able to analyse the free energy of dimer interaction], but apparently there's still something wrong. I had hoped that if VMD can display a prmtop/inpcrd file, it's correctly formatted for NAMD... Thanks!Irene Newhouse

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