VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Thu Jun 27 2013 - 16:12:27 CDT

Yes, that was the problem. the parameter file.
Thanks!
Eddie

On Thu, Jun 27, 2013 at 3:56 PM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

> That is “may not”****
>
> ** **
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Bennion, Brian
> *Sent:* Thursday, June 27, 2013 12:54 PM
> *To:* eackad_at_siue.edu; Mayne, Christopher G
> *Cc:* Vmd l
> *Subject:* RE: vmd-l: fftk Opt. Charges****
>
> ** **
>
> You man not have an atom name of C3, but you may have an atom type in your
> parameter file that is labeled C3. Maybe you meant CT3 and it is just a
> typo?****
>
> ** **
>
> Brian****
>
> ** **
>
> ** **
>
> *From:* Prof. Eddie [mailto:eackad_at_siue.edu <eackad_at_siue.edu>]
> *Sent:* Thursday, June 27, 2013 12:37 PM
> *To:* Mayne, Christopher G
> *Cc:* Bennion, Brian; Vmd l
> *Subject:* Re: vmd-l: fftk Opt. Charges****
>
> ** **
>
> Any ideas?****
>
> ** **
>
> On Wed, Jun 19, 2013 at 1:16 PM, Prof. Eddie <eackad_at_siue.edu> wrote:****
>
> Thanks Christopher! That worked. Now the optimization runs.****
>
> ** **
>
> However, the optimization now crashes and says:****
>
> ** **
>
> can't read "ljPars(C3)": no such element in array****
>
> can't read "ljPars(C3)": no such element in array****
>
> while executing****
>
> "lindex $ljPars($aType) 0"****
>
> (procedure "::ForceFieldToolKit::ChargeOpt::computeIntE" line 33)****
>
> invoked from within****
>
> "::ForceFieldToolKit::ChargeOpt::computeIntE $i $j"****
>
> (procedure "::ForceFieldToolKit::ChargeOpt::optCharges" line 77)****
>
> invoked from within****
>
> "$function $p0list"****
>
> (procedure "construct_initial_complex" line 13)****
>
> invoked from within****
>
> "construct_initial_complex [lindex $args 0]"****
>
> (procedure "::Optimize::Opt1::handle" line 89)****
>
> invoked from within****
>
> "$opt initsimplex [lrange $chargeInit 0 end-1] "****
>
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 409)****
>
> invoked from within****
>
> "::ForceFieldToolKit::ChargeOpt::optimize"****
>
> ** **
>
> I don't have any atom names C3 and I don't end up getting any results. Any
> ideas?****
>
> Thanks for the help!****
>
> Eddie****
>
> ** **
>
> On Wed, Jun 19, 2013 at 10:53 AM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:****
>
> ffTK generates Gaussian input files for computing water interaction
> energies at each interaction site with the following syntax: ****
>
> ** **
>
> RESNAME-(ACC | DON)-ATOMNAME.gau****
>
> ** **
>
> There are special cases (e.g., carbonyl oxygens) in which three
> interaction input files are generated. These position the water molecule
> 180 degrees and +/-120 degrees with respect to the C=O bond and have the
> following syntax for the 120 degree orientations:****
>
> ** **
>
> RESNAME-(ACC | DON)-ATOMNAME-(120a | 120b).gau****
>
> ** **
>
> When importing the target data into the QM Target Data section of the
> Charge Opt. tab, ffTK parses the filename to pull out the atom name, which
> is needed during the optimization. For these 120 degree files, the parser
> don't quite do this right, and the atom name gets parsed as ATOMNAME-120(a
> | b). In the target data box, simply modify the column for the atom name
> to remove the -120(a | b) portion, yielding a valid atom name.****
>
> ** **
>
> ** **
>
> Regards,****
>
> Christopher Mayne****
>
> ** **
>
> ** **
>
> On Jun 19, 2013, at 8:50 AM, Prof. Eddie wrote:****
>
> ** **
>
> 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 ****
>
> ** **
>
>
>
> ****
>
> ** **
>
> --
> _________________________________________________________
> 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 ****
> 

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