VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Jun 27 2013 - 14:53:35 CDT

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]
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<mailto: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<mailto: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<mailto: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<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of Prof. Eddie [eackad_at_siue.edu<mailto: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<tel:%28618%29%20650-2390>
--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390<tel:%28618%29%20650-2390>
--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390<tel:%28618%29%20650-2390>
--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390