Aron,
Thanks. I discovered it by myself that deleting these two sections causes no harm, but I was wondering about two things.
One is whether setting OldPrmtopFormat to on will do the trick?
The other is whether the AMBER developers would bring it to the attention of the NAMD people to introduce a change in their code to make the use of the amber topology file easier with NAMD. I suppose it might be easier this way.
Rami
On Jan 9, 2012, at 12:44 PM, Ben Roberts wrote:
Hi Rami,
Further to Adrian's remarks, these sections in the prmtop are relatively recent additions (i.e., within the last year or two). Before then, the parameters they govern (SCEE and SCNB) were entered in the simulation configuration file (the "mdin", in Amber jargon).
It seems that the NAMD developers haven't yet updated their prmtop parser to accommodate the latest specs.
Ben
On 9/01/2012, 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
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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 - 10:30:04 PST
