VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Wed Jun 19 2013 - 08:50:47 CDT

The water Int. part of fftk generated these names. It made a bunch of
O-120a or OAV-12a etc. how would I find that label and why would the water
Int. part of fftk generate that? Molfracture does not show anything by that
name.
Thanks,
Eddie

On Tue, Jun 18, 2013 at 5:47 PM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

> Is there an atom name with the label O-120a ?
>
> I doubt it, once you load in all the log files you have to make sure and
> rename the labels so that they refer to an actual atom. You will have
> several labels for the oxgygen atom that are identical although the log
> files are different.
> Brian
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Prof. Eddie [eackad_at_siue.edu]
> *Sent:* Tuesday, June 18, 2013 2:47 PM
> *To:* Vmd l
> *Subject:* vmd-l: fftk Opt. Charges
>
> Hi all,
> I generated all the water interactions with my ligand using gaussian. I've
> setup everything tin fftk in the opt. charges part. I then try to optimize
> using the default (or simulated annealing as I get the same error for
> both):
>
> atomselect: cannot parse selection text: name O-120a and resname LIG
> while executing
> "atomselect $refmolid "name [lindex $atomList $i] and resname $resName"
> frame $i"
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 213)
> invoked from within
> "::ForceFieldToolKit::ChargeOpt::optimize"
> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
>
> The file is there (Lig-Acc-O-120a.log/chk) and the log says it had
> finished. Is this a problem of quotation or something? I am using vmd
> 1.9.2a26.
> Thanks,
> Eddie
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390