VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Thu Jun 27 2013 - 14:37:15 CDT

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