VMD-L Mailing List

From: Minh Ho (minhho_at_umass.edu)
Date: Wed Oct 07 2020 - 10:22:21 CDT

Thank you, I will try that!

On Wed, Oct 7, 2020 at 11:21 AM Spivak, Mariano Alejo <mspivak_at_illinois.edu>
wrote:

> Dear Minh,
>
> It is definitely a trick problem, I don’t think increasing maxIter will
> solve the problem.
> You might try taking the initial structure and try rotating the water so
> that it sits perpendicular to the ring plane.
>
> Hope this helps
>
> Best
>
> On Oct 7, 2020, at 10:12 AM, Minh Ho <minhho_at_umass.edu> wrote:
>
> Dear Mariano Alejo,
>
> Thank you very much! I just noticed the issue too. When I looked at the
> initial position of the water interacting with H7, it was in close range
> with nearby water molecules. Is this an issue when calculating water
> interaction? Or is it *not* the issue because the water interaction
> calculation is done separately for each hydrogen bond donor/acceptor? To
> fix the problem, should I increase *maxIter* values and wait for the
> water interaction at H7 converge? Or should I rearrange position of the
> water molecule interacting with H7?
>
> Sincerely,
> Minh
>
> On Wed, Oct 7, 2020 at 11:03 AM Spivak, Mariano Alejo <
> mspivak_at_illinois.edu> wrote:
>
>> Dear Mihh,
>>
>> I was able to reproduce your error with your files.
>> I believe the issue is that one of the water interaction calculations
>> (CAFF-DON-H7.log) has not converged.
>>
>> Best
>>
>> > On Oct 6, 2020, at 10:36 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>> >
>> > Indeed, the new versions support ORCA. I'll ask one of the FFTK
>> developers
>> > to comment on this further.
>> >
>> > Best,
>> > John Stone
>> >
>> > On Fri, Oct 02, 2020 at 07:44:37PM -0400, Minh Ho wrote:
>> >> Dear Daniel,
>> >>
>> >> VMD-1.9.4 does support both Gaussian and ORCA for QM calculations.
>> >> On Fri, Oct 2, 2020 at 7:39 PM Daniel Fellner
>> >> <[1]dfel694_at_aucklanduni.ac.nz> wrote:
>> >>
>> >> Someone can correct me if I'm mistaken, but I believe FFTK requires
>> >> Gaussian for the QM calculations?
>> >> Daniel Fellner BSc(Hons)
>> >> PhD Candidate
>> >> School of Chemical Sciences
>> >> University of Auckland
>> >> Ph +64211605326
>> >> On Sat, Oct 3, 2020 at 12:31 PM Minh Ho <[2]minhho_at_umass.edu>
>> wrote:
>> >>
>> >> Hi all,
>> >>
>> >> I am new to using FFTK and ORCA to parameterize a small
>> molecule. I am
>> >> following the screencast FFTK tutorial at:
>> >> [3]http://www.ks.uiuc.edu/Research/fftk/. I am experiencing some
>> >> errors at step "charge 2" after calculating water interactions
>> (charge
>> >> 1). The errors is as follows:
>> >>
>> >> atomselect set: 0 data items doesn't match 1 selected atoms.
>> >> atomselect set: 0 data items doesn't match 1 selected atoms.
>> >> Â Â while executing
>> >> "$temp set x [lindex [lindex $molCoords $i] 0]"
>> >> Â Â (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line
>> 191)
>> >> Â Â invoked from within
>> >> "::ForceFieldToolKit::ChargeOpt::optimize"
>> >> Â Â (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
>> >> Â Â invoked from within
>> >> "::ForceFieldToolKit::gui::coptRunOpt "
>> >> Â Â invoked from within
>> >> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
>> >> Â Â 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..."
>> >> Â Â (command bound to event)
>> >> I have attached the link to a zip file including all inputs
>> necessary
>> >> to reach the charge opt. step using FFTK here:
>> >> [4]
>> https://drive.google.com/file/d/1uOyUriIJN7i1KiXo2Xs9nTPgC6w5ztyV/view?usp=sharing
>> >>
>> >> Anyone's help + explanation would be greatly appreciated.
>> >>
>> >> Sincerely,
>> >> Minh
>> >> P.S. I am using VMD-1.9.4a43 and ORCA 4.0.1.2
>> >> --
>> >> Minh Ho
>> >> BS Biochemistry, Class of 2021
>> >> Department of Biochemistry and Molecular Biology
>> >> University of Massachusetts Amherst
>> >>
>> >> --
>> >> Minh Ho
>> >> BS Biochemistry, Class of 2021
>> >> Department of Biochemistry and Molecular Biology
>> >> University of Massachusetts Amherst
>> >>
>> >> References
>> >>
>> >> Visible links
>> >> 1. mailto:dfel694_at_aucklanduni.ac.nz
>> >> 2. mailto:minhho_at_umass.edu
>> >> 3. http://www.ks.uiuc.edu/Research/fftk/
>> >> 4.
>> https://drive.google.com/file/d/1uOyUriIJN7i1KiXo2Xs9nTPgC6w5ztyV/view?usp=sharing
>> >
>> > --
>> > NIH Center for Macromolecular Modeling and Bioinformatics
>> > Beckman Institute for Advanced Science and Technology
>> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> > http://www.ks.uiuc.edu/Research/vmd/
>> >
>>
>>
>
> --
> *Minh Ho*
> BS Biochemistry, Class of 2021
> Department of Biochemistry and Molecular Biology
> University of Massachusetts Amherst
>
>
> 

-- 
*Minh Ho*
BS Biochemistry, Class of 2021
Department of Biochemistry and Molecular Biology
University of Massachusetts Amherst