VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jun 04 2012 - 04:10:40 CDT

DIRECTED TO SUCCESSFUL USERS OF FFTK OptCharges Section:

For a small organic molecule, the WaterInt section was completed
successfully for the groups that interact with water most. OptCharges
halts. Equalizing charges was restricted to a carboxylate; C-H were
not equalized. The debugging log shows what was done:

==========================================
 Charge Optimization GUI Debugging Output
==========================================
INPUT SECTION
psfPath: /home/francesco/..../CLV.psf
pdbPath: /home/francesco/....CLV_optimized.pdb
resName: CLV
parList:
        /home/francesco/..../par_all27_prot_lipid.prm
        /home/francesco/..../CLV_gaffchanged.prm
        /home/francesco/..../CLV_fftk.prm
namdbin: namd2
log file: ChargeOpt.log
-------------------------------------------
CHARGE CONSTRAINTS SECTION
chargeGroups: {O4 O5}
chargeInit: -0.8023
chargeBounds: {-1.0 1.0}
chargeSum: -1.003
-------------------------------------------
QM TARGET DATA SECTION
baseLog: /home/francesco/work_3LEZ_charmm27FF/mod2-CLV_FFTK_CHARMM/single-point_energy.log
watLog: /home/francesco/work_3LEZ_charmm27FF/mod2-CLV_FFTK_CHARMM/single-point_energy_water.log
logFileList:
        /home/francesco/....../CLV-ACC-O1.gau.log
        /home/francesco/...../CLV-ACC-O1-m120.gau.log
        /home/francesco/...../CLV-ACC-O1-p120.gau.log
        /home/francesco/..../CLV-ACC-O4.gau.log
        /home/francesco/...../CLV-ACC-O4-m120.gau.log
        /home/francesco/........./CLV-ACC-O4-p120.gau.log
        /home/francesco/......../CLV-ACC-O5.gau.log
        /home/francesco/......../CLV-ACC-O5-m120.gau.log
        /home/francesco/.........../CLV-ACC-O5-p120.gau.log
        /home/francesco/........./CLV-DON-H8.gau.log
atomList: O1.gau O1-m120.gau O1-p120.gau O4.gau O4-m120.gau
O4-p120.gau O5.gau O5-m120.gau O5-p120.gau H8.gau
indWeights: 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
-------------------------------------------
ADVANCED SETTINGS SECTION
start: -0.4
end: 0.4
delta: 0.05
end: 0.4
offset: -0.2
scale: 1.16
tol: 0.005
dWeight: 1.0
Optimization mode: downhill
Simulated Annealing Parameters: Temp. 25, Steps 20, Iterations 15
Override ReChargeFromPSF: 0
Override Charges:
debug: 1
==========================================

Single Point Energies Parsed. QME(water):
-47665.049422800854 QME(cmpd): -461756.39140976494
Cmpd atoms retyped to: KY KY Z K W K3 K2 K2 WS K W W K3 WJ JW JK JK J2
J1 JA J1 J1
Cmpd atoms recharged to: -0.22939999401569366 0.21549999713897705
-0.3328000009059906 0.6535000205039978 -0.5724999904632568
-0.08609999716281891 0.10090000182390213 -0.3012000024318695
-0.3549000024795532 0.9506000280380249 -0.802299976348877
-0.802299976348877 0.18960000574588776 -0.6248000264167786
0.40700000524520874 0.07620000094175339 0.07620000094175339
0.1137000024318695 0.08969999849796295 0.15800000727176666
0.03620000183582306 0.03620000183582306

********
The RunOpt log tells that neither the atom names, nor the residue
name (which ones I had set, as shown above) could be parsed:

atomselect: cannot parse selection text: name O1.gau and resname CLV
atomselect: cannot parse selection text: name O1.gau and resname CLV
    while executing
"atomselect top "name [lindex $atomList $i] and resname $resName" frame $i"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 152)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} {
.fftk_gui.hlf.nb.chargeopt.runOpt state !pressed;
.fftk_gui.hlf.nb.chargeopt.runOpt in..."
    (command bound to event)

******************

If you look at the last part of the debugging log, you see "Cmpd atoms
retyped to: KY KY Z K W ...." In fact, I came to FFTK with psf/pdb
generated from antechamber-gaff/charmgen, which works fine for psf/pdb
toward namd. Are perhaps such gaff atom types confusing FFTK? What do
you have there in place of my "KY KY Z K W.."? Or do you see any
overlooking/misinterpretation in my doing?

Thanks

francesco pietra