VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu May 30 2013 - 10:17:42 CDT

I would suggest a fragment based approach to your validation.

I'm pretty sure that I've determined the cause of your current error. This happens when running sequential optimizations without clearing the results box, changing the number of atoms that are included in the optimization from the preceding run. This is a bug; I will try to address it prior to the final 1.9.2 final release. In the meantime, if you change the number of atoms that are included in the optimization, first clear the results from any previous runs.

The HF single point calculation is used to compute the interaction energy. The MP2 single point calculation is used to obtain the dipole moment.

Regards,
Christopher Mayne

On May 30, 2013, at 6:11 AM, surya narayanan chandrasekaran wrote:

Hi,
There are enough literature for the system containing complete FF parameter. but our idea is to validate the FF for a specific purpose. Anyway i am now doing step by step approach. So I overcome previous error. But these is the new error:

expected floating-point number but got ""
expected floating-point number but got ""
    while executing
"format %1.3f [lindex $finalCharges $i]"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 439)
    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)

This is what it shows in terminal window.
90: -0.4164819391643594 -0.057477495153048785 0.04425565463821317 -0.04191889719449131 -0.03481122763731818 -0.08942319851969328 0.04624171937672228 -0.1037705831593676 -0.014231337054360645 -0.0057994098986916525 0.03862315687543251 0.12966829397588905 0.11067876264771703 0.027788216398095696 0.040788325942648355 -0.015899829304677787 0.12501753558669915 -0.03544481078109548 0.08173920850142705 0.024192034588308806 -0.12295625392651034 -0.12155047959722978 0.05367113097357905 -0.09597356868730267 -0.020710520912424358 0.023326016393429752 -0.11162853863295871 -0.007998571794961435 -0.051965910192716125 -0.12441090312713943 0.009197343605752398 0.06369351347099475 0.024741817301706385 0.13678531780791645 0.11745584123024622 0.10200486328480991 -0.014086643959677996 -0.0006409063310558981 -0.10869521817879997 -0.09276830393544586 0.0021942174951089964 -0.005008105141057144 -0.20451319869279386 0.0418878010463012 -0.09787333093664699 0.056488065820808946 --> 920155169687.4338
91: -0.23815028187034218 -0.06525103392227471 -0.028171832141816337 0.04382305191973589 0.0027100264636047595 -0.029757812169598122 -0.06117955141692656 0.01847534503385144 0.03870201348521461 -0.012656532493677018 0.04429190563355304 -0.005814581663292849 -0.003565664460958096 0.022831528883827088 -0.03189996406198106 0.03589885960661436 0.04494775796972928 0.07336468402161539 0.039455852232268246 -0.09782686370859789 -0.033467011704375285 -0.007640869309604292 -0.06341002503057755 -0.05214537453043942 -0.013774323263891821 -0.031170266091422837 -0.07877024630734503 0.022765472573900415 -0.011540892646115849 -0.045763900882304503 -0.019793397545142602 -0.008902055179125186 0.009253131572992993 0.023548753794983387 0.02269153257719715 0.0024714908783821554 0.030113435215437967 -0.010926915334122097 0.029260463971165617 0.0017617155754303913 -0.03617586047344796 -0.0031835879545550026 -0.1495432647529804 0.0542117078402133 -0.030551485775961323 -0.02307231596308209 --> 920176214587.2339
Simulated annealing:
Initial temperature T0=25.0
Number of T cycles Tsteps=20
Simulated annealing step 0: T=25.0
Already converged after T=25.0
Simulated annealing step 1: T=0
Simulated annealing converged.

I tried in two ways still getting the same error?
1)What i did is calculated charges without hydrogen atoms but including charge file for hydrogen interacting water molecule same error comes.
 2) Removing hydrogen interaction water molecule charge file and run the simulation. same error.

once i tried the complete system too but i am getting the same error.

I think its a minor mistake some where. if you can help then it will be great full.
here are the list of files i loaded you can recreate it from my previous dropbox link
 BCL-ACC-C1A.log BCL-ACC-C4D.log BCL-ACC-ND.log BCL-DON-C2D.log BCL-DON-CHB.log BCL-DON-HAA2.log BCL-DON-HBD.log BCL-DON-HMC3.log BCL-ACC-C1B.log BCL-ACC-CAD.log BCL-ACC-O1A.log BCL-DON-C3B.log BCL-DON-CHC.log BCL-DON-HAC1.log BCL-DON-HCH.log BCL-ACC-C1C.log BCL-ACC-CGA.log BCL-ACC-O1D.log BCL-DON-C3D.log BCL-DON-CHD.log BCL-ACC-C1D.log BCL-ACC-CGD.log BCL-ACC-O2A.log BCL-DON-C4A.log BCL-ACC-C2B.log BCL-ACC-CHA.log BCL-ACC-O2D.log BCL-DON-C4B.log BCL-ACC-C2D.log BCL-ACC-CHB.log BCL-ACC-OBD.log BCL-DON-C4C.log BCL-ACC-C3B.log BCL-ACC-CHC.log BCL-DON-C1A.log BCL-DON-C4D.log BCL-ACC-C3D.log BCL-ACC-CHD.log BCL-DON-C1B.log BCL-DON-CAD.log BCL-DON-O45.log BCL-ACC-C4A.log BCL-ACC-NA.log BCL-DON-C1C.log BCL-DON-CGA.log BCL-ACC-C4B.log BCL-ACC-NB.log BCL-DON-C1D.log BCL-DON-CGD.log BCL-ACC-C4C.log BCL-ACC-NC.log BCL-ACC-OBB.log BCL-DON-C2B.log BCL-DON-CHA.log BCL-ACC-CAB.log BCL-DON-CAB.log

also i would like to state. how i overcome the previous error maybe it will be helpfull for others.
1) one of the atom name Oxygen has been replaced by FFTK to carbon and after doing the RHF calculation the water molecule just bounces out and i got a trajectory of 50 frames for the step so i removed it.
2) Aother error is really stupid like the toolkit creates some file with 120a and 120b for the same atom name when you load the optimized file into the next step it creates an error "atom name" has multiple bonds. so i removed that file too.

since quantum calculation computes charges for all the atoms you dont really need to worry placing water molecule for each atom. but it would be really helpful if its clearly stated in the journal of FFTK how exactly the final charges are computed from each file.

I am also not clear about the what it does with single point calculation charges from HF and MP calculations.

On Tue, May 28, 2013 at 7:13 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
Suryanarayanan,

1)
a. The bond visualization is purely a visualization issue that has to do with how VMD guesses bonds based on the first frame. It will not affect the actual charge optimization routine.
b. the number of frames is related to the number of steps taken during the QM optimizations. Some water molecules are positioned near an energy minimum, others will have to be optimized more.

2)
I was able to reproduce your error. I also found that only including one or two of the log files resolved the error. The error message suggests that VMD the measure bond contains too few or too many atom indices. Based on these observations I can think of two possibilities:

when loading the QM target data, the parser assigns an inappropriate atom name (i.e. the atom name doesn't exist)
or
there are two atoms with the same name

beyond this particular syntax error that's hanging ffTK up, I suspect that you are trying to do waaaaaaay too much here. The best approach to parameterization is the so-called "divide and conquer" approach. I would also encourage you to look through the literature to try and find validated parameters for heme and/ or porphyrin rings.

Regards,
Christopher Mayne

On May 27, 2013, at 11:02 AM, surya narayanan chandrasekaran wrote:

Hi,

I was trying to develop force field for a phorphrin magnesium complex. When i was in the charge optimization step i am having two kinds of problem.

1) some of the water molecule after first step of RHF calculation seems to be bonded on visualization and the number of frames for energy minimization also pretty less compared to other water molecule number of frames. I cross checked the initial file(.gau) for calculation its perfectly fine. anyway Gaussian does not showed it as an error neither the FFTK.

2)I am getting this error during opt.charges step. I am sending you the link of PSF PDB PAR and log files in dropbox kindly have a look at it if you want.

  measure bond: must specify exactly two atoms in a list
 measure bond: must specify exactly two atoms in a list
    while executing
"measure bond "[$temp1 get index] [$temp2 get index]" frame $i"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 215)
    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)

https://www.dropbox.com/sh/6klo7fzbgshgtnk/LpfqxDz-Pf/forcefield?n=106188702 

--
Suryanarayanan C
M.S Chemist
+94-01794019116
--
Suryanarayanan C
M.S Chemist
+94-01794019116