VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Jan 24 2019 - 13:37:07 CST

Sorry for the slow responses on this.

I don't appear to be able repeat this error with a recent download of VMD
1.9.3 with parseFEP 1.9.2. Similar results for 1.9.4a (which is actually
probably more stable from the perspective of parseFEP).

Can you send me your terminal output?

On Fri, Jan 18, 2019 at 12:32 AM surya narayanan chandrasekaran <
sonofsunsurya_at_gmail.com> wrote:

> Hi,
>
> Thanks for the suggestion, But both of the solutions didnot work. I had
> vmd 1.94 previously i removed it and installed 1.93 supposibly the stable
> version and loaded the example output files given in the tutorial. the same
> error.
> I have ubuntu16.04 in my laptop with vmd 1.94 in it. the same error.
>
> I have tried if there is any other problem between vmd and xmgrace, for
> example i saved my RMSD using multiplot.agr the plot immediately opened in
> xmgrace.
>
> y dont vmd implement multiplot for this job.
>
>
>
>
> On Thu, Jan 17, 2019 at 6:27 PM soroush ziaei <soroush.ziaei7337_at_gmail.com>
> wrote:
>
>> Hi,
>>
>> because of some problems and many features that have been changed in the
>> newer version, My suggestion is to work with Ubuntu 16.04 LTS instead of
>> 2018 version.
>>
>> By the way, I have loaded these files a few minutes ago into fep plugin
>> of VMD and easily plotted these values with xmgrace. I think your problem
>> is related to loading file!
>>
>> Please load <aqua-forward-on.fepout> & <aqua-backward-on.fepout>.
>>
>> I hope to done.
>>
>>
>>
>> Regards,
>>
>> soroush
>>
>>
>>
>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
>> Windows 10
>>
>>
>>
>> *From: *surya narayanan chandrasekaran <sonofsunsurya_at_gmail.com>
>> *Sent: *Wednesday, January 16, 2019 4:58 PM
>> *To: *vmd-l_at_ks.uiuc.edu
>> *Subject: *vmd-l: FEP tutorial plot error
>>
>>
>>
>> Hi,
>>
>>
>>
>> I was doing alchemical FEP tutorial. After doing the forward and
>> backward step i was trying to analyse the .fepout in the vmd plugin and got
>> the below error. My computer is Linux based (ubuntu 18) and i have xmgrace
>> and gnuplot installed in it.
>>
>>
>>
>> option i selected in the plugin:
>>
>> TEMP:300
>>
>> GRM-Charlier: 0
>>
>> disp (on) for unix ststems only
>>
>> forward and backward .fepout file loaded
>>
>> BAR-estimator
>>
>>
>>
>> Error: missing close-bracket
>>
>>
>> missing close-bracket
>> while executing
>> "set lambda1 [format "%8.4f" [lindex $::ParseFEP::fwd_lambda $index]
>> set lambda2 [format "%8.4f"
>> [lindex ..."
>> invoked from within
>> "if { [file exists [format "file%d.dat" $file_index] ] } {
>> set lambda1 [format "%8.4f"
>> [lindex $::ParseFEP:..."
>> (procedure "::ParseFEP::fepdisp_unix" line 321)
>> invoked from within
>> "::ParseFEP::fepdisp_unix "
>> (procedure "namdparse" line 47)
>> invoked from within
>> "namdparse"
>> (in namespace inscope "::ParseFEP" script line 16)
>> invoked from within
>> "::namespace inscope ::ParseFEP {
>>
>> if { [string length $::ParseFEP::fepofile] < 1 } {
>> tk_dialog .errmsg {NamdPlot Error} "No ..."
>> invoked from within
>> ".parseFEP.runbutton invoke"
>> ("uplevel" body line 1)
>> invoked from within
>> "uplevel #0 [list $w invoke]"
>> (procedure "tk::ButtonUp" line 22)
>> invoked from within
>> "tk::ButtonUp .parseFEP.runbutton"
>> (command bound to event)
>>
>>
>>
>>
>> --
>>
>> Warm regards,
>>
>> Dr. Suryanarayanan C
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> Warm regards,
> Dr. Suryanarayanan C
> DST-Inspire Faculty,
> Department of Chemistry,
> National Institute of Technology, Trichy, India 620015.
> Mobile: +91-8608908117 <089396%2008173>
>
>