Hi Rami,
Just to second Adrian, NAMD just needs to update the code for reading AMBER
files. The addition of those two flags which allow you to set the scaling
coefficients for individual elements is a relatively new addition to AMBER
and it hasn't made its way into NAMD yet.
The response you will get from the NAMD community is to do exactly as you
did, remove those two lines. There are no problems associated with that.
On a side note, if you are using AMBER forcefields with NAMD make sure you
have set the scaled1-4 variable to be 0.83333 instead of the default 1.0.
~Aron
On Mon, Jan 9, 2012 at 12:41 PM, Adrian Roitberg <roitberg.ufl.edu> 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>
> > http://atlas.physbio.mssm.edu/~osmanlab
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 09 2012 - 10:30:02 PST
