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>
> http://atlas.physbio.mssm.edu/~osmanlab
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Mon Jan 09 2012 - 10:00:04 PST
