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Sam,
I tried sending an email to rnatoolbox-help@simtk.org but the email
bounced. Below is the error message.
Kishor.
------------------------
This is the Postfix program at host mail.simtk.org.
I'm sorry to have to inform you that your message could not
be delivered to one or more recipients. It's attached below.
For further assistance, please send mail to <postmaster>
If you do so, please include this problem report. You can
delete your own text from the attached returned message.
The Postfix program
<rnatoolbox-help@simtk.org>: Command died with status 1:
"/var/www/html/simtk/cronjobs/forum_gateway.php rnatoolbox help". Command
output: local: fatal: execvp
/var/www/html/simtk/cronjobs/forum_gateway.php: No such file or directory
Final-Recipient: rfc822; rnatoolbox-help@simtk.org
Action: failed
Status: 5.0.0
Diagnostic-Code: X-Postfix; Command died with status 1:
"/var/www/html/simtk/cronjobs/forum_gateway.php rnatoolbox help". Command
output: local: fatal: execvp
/var/www/html/simtk/cronjobs/forum_gateway.php: No such file or directory
2009/6/17 Samuel Coulbourn Flores <scflores@stanford.edu>:
Well we have a bug report/feature request page. You can submit a feature
request by going to the RNAToolbox project page and clicking advanced ->
click Features & bugs -> select either features or bug -> click add new.
https://simtk.org/tracker/?group_id=359
As for your programming question, I can tell you how to add the feature you
want to your custom build, though it would be great if you could post it to
the help list.
Thanks
Sam
On Jun 16, 2009, at 9:14 AM, Kishor Bhalerao wrote:
Sam,
Do you want me to post the feature requests for RNABuilder on the
rnatoolbox forums ?
Kishor.
2009/6/15 Samuel Coulbourn Flores <scflores@stanford.edu>:
Hi Kishor,
Could you sign up for the rnatoolbox-help list, and ask this question there?
I will post my answer on there.
https://simtk.org/mailman/listinfo/rnatoolbox-help
Sam
On Jun 14, 2009, at 8:03 AM, Kishor Bhalerao wrote:
Hi Sam,
I have got it to work for the moment in a roundabout manner. Here is
the procedure i followed.
This time i downloaded the source from branches/v1_0 and rebuilt in
debug mode. (All my previous efforts were with the code obtained from
trunk)
In the ParameterReader.h, i changed the variable weldToGround from a
bool to an int to match with the ParameterReader.h from trunk/include
and also the corresponding line weldToGround = aToBool(mystring[0],
mystring[1].c_str() ); to atoi(mystring[1].c_str())
This change was more than sufficient to get it to work with all
commands other than SingleBondMobilityTorsion/Rigid/Free.
To include this command, i simply copied the corresponding lines from
the parameterReader.h and repel.h from trunk/include to the source in
branches/v1_0/include and copied the file setSingleBondMoblity.h from
trunk/include
I had another request. It seems to me that the RNABuilder.exe (Binary
for windows) which is currently available in the downloads section of
the RNABuilder website is not built from trunk but is built from
branches/v1_0 since it requires weldToGround as a bool and does not
support the command SingleBondMobilityTorsion/Rigid/Free. It would be
great if you can build this binary/executable which will support the
command SingleBondMobilityTorsion/Rigid/Free for windows and make it
available on RNABuilder website.
Thank you for your time.
Kishor Bhalerao
2009/6/13 Samuel Coulbourn Flores <scflores@stanford.edu>:
Hi Kishor,
We have not been able to reproduce your bug. As a last resort, how about if
you delete all of your RNABuilder source, check it out again, and rebuild?
Crazy, but very often works. You might try doing the same with Simbody,
though I'm much less confident that this will make a difference.
The best thing to do, I think, is to just check out an earlier revision of
RNABuilder. svn makes this easy. I don't think there are any recent
changes that benefit you all that much. I'm afraid Jack won't have time to
do much more than he has already.
Let me know if this works.
Sam
On Jun 12, 2009, at 9:21 AM, Kishor Bhalerao wrote:
Hi Jack,
find attached the file.
Regards,
Kishor.
On Fri, Jun 12, 2009 at 12:07 PM, Jack Middleton<jacklm@stanford.edu> wrote:
Hi Kishor,
I am having a hard time reproducing your bug.
Can you also send me the Base-interaction-paramters.4.csv file you are
using?
Thanks,
Jack
----- Original Message -----
From: "Kishor Bhalerao" <kishor8dm@gmail.com>
To: "Samuel Coulbourn Flores" <scflores@stanford.edu>
Cc: "Jack Middleton" <jacklm@stanford.edu>
Sent: Tuesday, June 9, 2009 5:50:53 PM GMT -08:00 US/Canada Pacific
Subject: Re: RNABuilder Bug ?
Hi Sam,
It still does not work for me. I have the latest version of rnatoolbox
which i was able to build and install without any errors. I got the
source from https://simtk.org/svn/rnatoolbox/trunk using svn. I do not
know what the -c option is. I am using MS Visual Studio Express
edition.
Next, I am certain it is reading my contacts.dat file, after reading
the file, the output is printed on the screen and i can clearly see
the comments i had inserted in the contacts.dat file.
The assert which fails is assert (myParameterReader2.lastStage >=
myParameterReader2.firstStage);
Now, i can very clearly see that the variables lastStage and
firstStage are still at the default value of 0 and 1 respectively and
have not been initialized to the values i set in the contacts.dat
file.
myParameterReader2.initialize("./contacts.dat");
cout<<"[RNABuilder.cpp] lastStage = "<<myParameterReader2.lastStage<<endl;
cout<<"[RNABuilder.cpp] firstStage =
"<<myParameterReader2.firstStage<<endl;
assert (myParameterReader2.lastStage >= myParameterReader2.firstStage);
I cannot get past this assert. Do you have any suggestions ?
Kishor
On Tue, Jun 9, 2009 at 7:45 PM, Samuel Coulbourn
Flores<scflores@stanford.edu> wrote:
Hi Kishor,
I just ran this and it runs fine. Looks like you have a tetraloop in there,
but no receptor. Are you sure you have the contacts.dat file in the
directory from which you are calling RNABuilder? are you using the -c flag?
Did you build from the latest revision in trunk?
Don't try to hack the code. I assure you, the problem is not in the code.
If you want I can try to log in to your machine and troubleshoot. However I
suspect your problem is a trivial one. I'm cc'ing Jack in case he has
something to say.
Sam
On Jun 6, 2009, at 3:52 PM, Kishor Bhalerao wrote:
Hi Sam,
I recently updated RNABuilder source and my contacts.dat file which
was working before fails. I have attached the file with this email.
assert (myParameterReader2.lastStage >=
myParameterReader2.firstStage); This is the assert which throws the
error. I checked the code and found that in the function
void ParameterReader::initializeDefaults() the variable currentStage
is not initialized to any value. Its commented out. This variable gets
used without being initialized on line 478 in the file
ParameterReader.h in the function
ParameterReader::initializeFromFileOnly()
I tried to set this value to 0 in the function initializeDefaults()
and now i get stuck at the assert(foundCoulomb); on line 319 in file
ParameterReader.h in function removeNonPriorityBasePairs().
Do you have any idea what am i doing wrong ?
Regards,
Kishor Bhalerao
PS : I have also tried setting currentStage = 1. ( My guess from the
name of the variables was that currentStage and FirstStage should have
identical default values.) On setting this value, The code fails after
printing
[Repel.h] About to fit RNA chain A.
Assertion failed: a.bodyIx.isValid(), file
..\..\src\DuMMForceFieldSubsystemRep.cpp, line 187
<contacts.dat>
Samuel Coulbourn Flores, PhD
Altman Lab
650.644.8416
花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国
<Base-interaction-parameters.4.csv>
Samuel Coulbourn Flores, PhD
Altman Lab
650.644.8416
花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国
Samuel Coulbourn Flores, PhD
Altman Lab
650.644.8416
花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国
Samuel Coulbourn Flores, PhD
Altman Lab
650.644.8416
花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国
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