From: Prof. Eddie (eackad_at_siue.edu)
Date: Wed Jun 19 2013 - 13:16:20 CDT

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