incompatibility between NAMD and amber topology files

From: Osman, Roman (
Date: Mon Jan 09 2012 - 16:13:24 CST

I am not sure whether I should post it to the amber mailing list or the namd. Since I created the topology file with leap I sent the message to the amber mailing list, but they suggested that I also send it to the NAMD list.

I wanted to bring to your attention that NAMD cannot read a topology file created by tleap in amber.
I prepared a regular topology file for a protein in a rectangular box using the ff99SB. NAMD complained with this message:

Reading parm file ( ...
PARM file in AMBER 7 format
FATAL ERROR: Failed to read AMBER parm file!
[0] Stack Traceback:
  [0] CmiAbort+0x5f [0xabb81b]
  [1] _Z8NAMD_diePKc+0x62 [0x509262]
  [2] _ZN9NamdState14configListInitEP10ConfigList+0xcad [0x90bab7]
  [3] _ZN9ScriptTcl9initcheckEv+0x5e [0x9753e0]
  [4] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x20 [0x971f9c]
  [5] TclInvokeStringCommand+0x91 [0xae0518]
  [6] /share/apps/NAMD_2.7b2/namd2 [0xb16368]
  [7] Tcl_EvalEx+0x176 [0xb169ab]
  [8] Tcl_EvalFile+0x134 [0xb0e3b4]
  [9] _ZN9ScriptTcl3runEPc+0x14 [0x9714da]
  [10] _Z18after_backend_initiPPc+0x22b [0x50da7b]
  [11] main+0x3a [0x50d81a]
  [12] __libc_start_main+0xf4 [0x301941d994]
  [13] _ZNSt8ios_base4InitD1Ev+0x4a [0x508bda]

Comparison of the current topology file with one that worked before finally focused on two additional sections that were not there before; these are:

When I removed those, NAMD read successfully the topology file and is running so far OK. I did not check the energies, but the behavior is of a normal NAMD job.

Perhaps it could be useful to introduce a fix in NAMD so it could read amber topology files without the need to manipulate them.

Thanks for your help,

Roman Osman
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
Tel: 212-659-8627
Fax: 212-849-2456

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