VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Sep 11 2014 - 11:17:17 CDT

Abhishek,

First of all, make sure that you are sending email to VMD-L from the exact same email address that you used to register, otherwise, the listserv will silently drop your email.

After taking a closer look at your input and error message, I recognized this as a parsing error due to changes in Gaussian keyword order in log files. The same error was reported by other users shortly after the 1.9.2a39 build was released and I subsequently committed a patch which appears to have resolved the error. This fix is included in the latest 1.9.2 alpha build currently posted to BioCoRE (1.9.2a42, Aug 28, 2014).

Please let me know if this error persists or you experience any other problems with the latest VMD builds.

Regards,
Christopher Mayne

On Sep 9, 2014, at 10:02 AM, Abhishek TYAGI wrote:

Dear Mayne,

Thankyou for your email, I have sanded the email to (vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>). I will wait for your reply.

regards

Abhishek

________________________________
From: Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>>
Sent: Tuesday, September 09, 2014 10:29 PM
To: Abhishek TYAGI
Subject: Re: FFTK: Opt Bonded error

Abhishek,

I searched VMD-L and wasn't able to find any of your postings (I also keep up with the listserv rather diligently), so it sounds like you either didn't properly register, or are sending from an email account that is different from the one you used to register.

At any rate, I took a quick look at your files and was able to reproduce your error. I'm quite busy for the next day or two and tracking these parsing errors down can take time. I will let you know when I have an idea what is going on.

Regards,
Christopher Mayne

On Sep 9, 2014, at 2:10 AM, Abhishek TYAGI wrote:

Hi,

(I am registered to vmd-1 list, I had sanded this email 3 times to vmd-1 mailing list, but I don’t get any reply, could you help me to the following questions.)

I had followed the tutorial, all the steps were run fine but in optimization Bonded I faced error as following:

I had followed the screencasts, but observed that the some information is not available in screencasts i.e for opt.bonded I cant find the link, otherwise in previous steps I can follow it easily. The information is a bit different for example:
1. In the 6-bonded.mov the procedure is different, but the VMD (version 1.9.2a39) on Ubuntu, it seems that the screencasts are for older version, which shows "Calculate Bonded Parameter", however, in new version Run Optimization is their. So while running opt. bonded I had successfully uploaded information asked, but when I started with parameters to optimize I had problem. What to do here??

2. Well I tried to guess and got following error: (what to do here?)

can't use empty string as operand of "*"
can't use empty string as operand of "*"
    while executing
"expr {3*$natoms}"
    (procedure "::QMtool::load_gaussian_log" line 50)
    invoked from within
"::QMtool::load_gaussian_log $hessLog $hessLogID"
    (procedure "::ForceFieldToolKit::gui::baoptGuessPars" line 46)
    invoked from within
"::ForceFieldToolKit::gui::baoptGuessPars "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.pconstr.fftkGuessPars invoke "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.pconstr.fftkGuessPars instate {pressed !disabled} { .fftk_gui.hlf.nb.bondangleopt.pconstr.fftkGuessPars state !pressed; ..."
    (command bound to event)

For your information I am uploading my input files. Please let me know how to proceed.

regards
Abhishek

<prid-init.par><prid-opt.pdb><prid-charged.psf><prid-hess.log>