Hi Adrian,
Thanks, but what is the solution?
I can always delete these two sections, but perhaps you as representative of amber could ask the NAMD team to fix this problem.
Best regards,
Rami
On Jan 9, 2012, at 12:41 PM, Adrian Roitberg wrote:
Hi Rami
It is a problem with namd !
The whole business with reading a prmtop file for amber is that you READ
the actual formats and flags from the file itself. NAMD seems to have a
very rigid definition of the contents of the prmtop file, so it does not
know what to do with the two sections you point to.
Adrian
On 1/9/12 12:38 PM, Osman, Roman wrote:
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><mailto:roman.osman.mssm.edu>
http://atlas.physbio.mssm.edu/~osmanlab
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu<mailto:roitberg.ufl.edu>
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http://lists.ambermd.org/mailman/listinfo/amber
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 - 10:00:05 PST
