From: Balazs Jojart (jojartb_at_gmail.com)
Date: Tue Feb 23 2010 - 03:33:24 CST
Dear Vlad, Francesco and Giacomo,
I faced to the same problem, and as Vlad suggested we compiled the namd
source code against tcl8.5, and we didn't obtained the ("FATAL ERROR:
syntax error in expression " $mdSteps == 0 && $mdStart eq "yes" " ) errors.
Unfortunatelly, the simulation stop with Segmentation Fault error
message, and it was reported previously by others, that there is
problems with the amber parm7/rst file using the namd2.7beta2 source
code. It means, that we have to use the CVS code?
Thank you for youer help in advance!
Balazs
Vlad Cojocaru wrote:
> Francesco, Giacomo,
>
> As I know this is an error coming from my RAMD scripts, I will curve
> in here .. (I changed the subject of the mail for the list archive)
>
> Recently users noticed that the RAMD scripts require tcl8.4 or above.
> I don't know what is the reason for that as I have never tested it
> against tcl 8.3 ... While running myself the scripts (self compiled
> NAMD against tcl8.4), I have never noticed the error Francesco and
> other users reported.
>
> The error is a complaint ("FATAL ERROR: syntax error in expression "
> $mdSteps == 0 && $mdStart eq "yes" " )
> about the following if statement at line 106 in the 'ramd-4.0_script.tcl':
>
> if { $mdSteps == 0 && $mdStart eq "yes" } {
> print "RAMD: WARNING: 'mdStart' has no meaning for pure RAMD
> simulation"
> }
>
> I do not see any problem with this if statement. Do any of you notice
> something in this statement that might not be compatible with tcl8.3 ?
> But maybe the error message is misleading ...
>
> Francesco, I don't know if this is too much of a trouble for you ...
> But if its possible, could you compile yourself the NAMD code against
> tcl8.4 or above and see if you get rid of the problem ? In the
> meantime, I will look to see if I can find the reason for this error .
>
> Cheers
> Vlad
>
>
> Giacomo Fiorin wrote:
>> Hi Francesco, if it were compiled against version 8.3 and you only
>> had 8.4 installed in the system, NAMD wouldn't find the 8.3 library
>> and wouldn't run at all. And even then, you can still install the
>> tcl8.3 package from lenny and try that out.
>>
>> Is it a tcl error or something else? NAMD's and Linux's version are
>> secondary informations, without the type of error message, it's
>> nearly impossible to help you.
>>
>> Giacomo
>>
>>
>> ---- ----
>> Giacomo Fiorin
>> ICMS - Institute for Computational Molecular Science
>> Temple University
>> 1900 N 12 th Street, Philadelphia, PA 19122
>> work phone: (+1)-215-204-4216
>> mobile: (+1)-267-324-7676
>> mail: giacomo.fiorin_at_gmail.com <mailto:giacomo.fiorin_at_gmail.com>
>> ---- ----
>>
>>
>> On Mon, Feb 22, 2010 at 9:38 AM, Francesco Pietra
>> <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>> wrote:
>>
>> Adding to myself, I have now tried NAMD_CVS_Linux-x86_64 2010-02-21
>> nightly build in place of namd_2.7b2. The TCL script does not work
>> either. Therefore, either the nightly build was compiled to TCL <8.4
>> (which would be surprising to me), or there is a problem with the TCL
>> script on Debian Linux amd64 lenny (stable).
>>
>> francesco
>>
>> On Mon, Feb 22, 2010 at 5:53 PM, Francesco Pietra
>> <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>> wrote:
>> > Please, which version of TCL was used in building amd64 binary
>> > namd_2.7b2? If <8.4, is the 22 Feb2010 nightly build compiled
>> against
>> > TCL 8.4?
>> >
>> > The problem is that a TCL script using version 8.4 does not
>> work with
>> > namd_2.7b2 (amd64).
>> >
>> > Thanks
>> >
>> > francesco pietra
>> >
>> >
>> >
>>
>>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> Heidelberg Institute for Theoretical Studies
> HITS gGmbH
> Molecular and Cellular Modelling Group
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> 69118 Heidelberg
>
> Tel: ++49-6221-533202
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]h-its.org
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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