VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Thu May 30 2013 - 06:11:28 CDT

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>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