Greetings,
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 thought it might be the responsibility of amber.
I wanted to bring to your attention that leap creates a topology file that is currently incompatible with NAMD.
I prepared a regular topology file for a protein in a rectangular box using the ff99SB. NAMD complained with this message:
Reading parm file (k7lp_r.top) ...
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:
%FLAG SCEE_SCALE_FACTOR and
%FLAG SCNB_SCALE_FACTOR
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.
Am I doing something wrong or is it a problem with leap.
Thanks for your help.
Rami
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
e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
http://atlas.physbio.mssm.edu/~osmanlab
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Received on Mon Jan 09 2012 - 10:00:03 PST
