VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Fri Oct 20 2023 - 09:32:45 CDT

Hi Joel,

You *did* add the new parameter file you made to your namd configuration
file, right? This looks like it should have worked to me.

-Josh

On 10/20/23 10:19 AM, Joel Subach wrote:
> ...hi and I updated the missing values to:
>
> IMPROPERS
> CG2O2 CG2R51 OG2D1 OG311 53.0000 0 0.00 !
>
> which were the values generated via CGenff in my .str file and the
> same Fatal Error:
>
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1
> OG311 (ATOMS 17 7 37 36)
> [Partition 0][Node 0] End of program
>
> (the input of a zaro value did not function and gave the sae error)
>
> I will try and start all over updating my parameter files while
> additionally using the partial charges tab, maybe this may repair this
> error, if you think of another way feel free to update me accordingly,
> thanks:)
> <https://urldefense.com/v3/__https://orcaforum.kofo.mpg.de/ucp.php?i=pm&mode=view&f=-2&p=2452*top__;Iw!!HXCxUKc!yIklqDtdzlcrx38jVlCoktFkWkrj7pHAbGfsypWihTjYHHF4zeTxLs5Pa9pj8K0RTjtBGC6XjzZtRlloomoeWL8$>
>
>
> On Sun, Oct 15, 2023 at 9:56 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
> ...and I did generate the DihOpt.log file regardless of the
> FATAL_ERROR (see--log file attached) although
> I am unsure if the FATAL-ERROR needs to be resolved first
> before proceeding?  Thanks:)
>
> On Sun, Oct 15, 2023 at 8:29 PM Joel Subach
> <mjsubach_at_alumni.ncsu.edu> wrote:
>
> ...and is this error possibly being generated via my .prm file
> not being filled out completely i.e. missing the ! and words?
> (See attached screenshot exhibiting the error file in the top
> right corner and the amended .prm file highlighted in center.)
>
> On Sun, Oct 15, 2023 at 6:49 PM Joel Subach
> <mjsubach_at_alumni.ncsu.edu> wrote:
>
> Hello JC thank you for your kind update:) and I changed
> the 0 to a O and precipitated the same error,
> please see screenshot attached exhibiting this error and
> its attached log.file in detail.  Thanks if you have
> a resolution to this problem:).
>
> On Sun, Oct 15, 2023 at 6:19 PM Gumbart, JC
> <gumbart_at_physics.gatech.edu> wrote:
>
> I believe that should be CG2O2, not CG202 (the letter
> O, not the number 0).  It can be hard to tell sometimes!
>
> Best,
> JC
>
>> On Oct 15, 2023, at 12:01 PM, Joel Subach
>> <mjsubach_at_alumni.ncsu.edu> wrote:
>>
>> Hello Josh thank you for your kind update:).
>>
>> I amended, as you had recommended, the .prm file
>> generated during my initial ffTK run and precipitated
>> the same error
>> (see screenshot attached labeled FATAL ERROR where at
>> the top-right you can read the error and the bottom
>> right
>> exhibits my modified .prm file as recommended, on the
>> left is the OPT Torsion GUI.  Also attached is the
>> complete error-
>> log file for your inspection. Thanks if you can help:)
>>
>> Best,
>> Joel 🚀
>>
>> On Sat, Oct 14, 2023 at 7:15 PM Vermaas, Josh
>> <vermaasj_at_msu.edu> wrote:
>>
>> Hi Joel,
>>
>> Take a look at par_all36m_prot.prm from the
>> standard CHARMM parameter file. There will be an
>> improper section that you can crib from. A
>> typical line will look something like this:
>>
>> HR1  NR1  NR2  CPH2    0.5000  0      0.0000
>>
>> You'd change the 4 atomtypes to be what you need
>> them to be for your system, and then make the 0.5
>> (the force constant for the improper energy) 0.
>>
>> -Josh
>>
>> On 10/14/23, 11:37 AM, "owner-vmd-l_at_ks.uiuc.edu
>> <mailto:owner-vmd-l_at_ks.uiuc.edu> on behalf of
>> Joel Subach" <owner-vmd-l_at_ks.uiuc.edu
>> <mailto:owner-vmd-l_at_ks.uiuc.edu> on behalf of
>> mjsubach_at_alumni.ncsu.edu
>> <mailto:mjsubach_at_alumni.ncsu.edu>> wrote:
>>
>>
>> Hello JC thank you so much for teaching me via
>> your kind update:).
>>
>>
>> Can you please be more specific in this
>> modification since I have never
>> done this before, below is my .par existing file:
>>
>>
>> IMPROPER
>> !
>> !V(improper) = Kpsi(psi - psi0)**2
>> !
>> !Kpsi: kcal/mole/rad**2
>> !psi0: degrees
>> !note that the second column of numbers (0) is
>> ignored
>> !
>> !atom types Kpsi psi0
>> !
>>
>>
>> i.e. how would you suggest to modify the above
>> i.e. add the dummy improper
>> with a force constant of zero?
>>
>>
>> Thanks if you can:)
>> Joel 🚀
>>
>>
>> On Sat, Oct 14, 2023 at 4:49 AM Gumbart, JC
>> <gumbart_at_physics.gatech.edu
>> <mailto:gumbart_at_physics.gatech.edu>>
>> wrote:
>>
>>
>> > Hi Joel,
>> >
>> > You could just manually add a dummy improper
>> with a force constant of zero
>> > for now. You can then optimize the improper
>> after getting the dihedrals.
>> >
>> > Best,
>> > JC
>> >
>> > On Oct 13, 2023, at 7:52 AM, Joel Subach
>> <mjsubach_at_alumni.ncsu.edu
>> <mailto:mjsubach_at_alumni.ncsu.edu>> wrote:
>> >
>> > Hello VMD Community, towards the above topic:
>> >
>> > Via the ffTK Opt Torsions Tab to optimize
>> dihedral parameters (Tutorial 6.2
>> > link:
>> *https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$
>> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$>
>>
>> >
>> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$
>> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$>
>> >).*
>> >
>> > I had clicked Run Optimization after inputting:
>> >
>> > all of the proper files i.e. psf, pdb, par for
>> the *input section *
>> >
>> > my 4-output.out resulting files generated via
>> ORCA for the *QM Target
>> > Data Section*
>> >
>> > and my atom types for my two-dihedral angles
>> for the *Dihedral Parameter
>> > Settings*
>> >
>> > the below error states:
>> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS
>> FOR CG2O2 CG2R51 OG2D1
>> > OG311 (ATOMS 17 7 37 36)
>> > [Partition 0][Node 0] End of program
>> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS
>> FOR CG2O2 CG2R51 OG2D1
>> > OG311 (ATOMS 17 7 37 36)
>> >
>> > (See complete Application_Error.log file
>> attached and note within it the: *Info:
>> > 0 IMPROPER*
>> > may have been generated via ffTK?)
>> >
>> > Below is a paste of the impropers from my
>> generated .par file:
>> >
>> > IMPROPER
>> > !
>> > !V(improper) = Kpsi(psi - psi0)**2
>> > !
>> > !Kpsi: kcal/mole/rad**2
>> > !psi0: degrees
>> > !note that the second column of numbers (0) is
>> ignored
>> > !
>> > !atom types Kpsi psi0
>> > !
>> >
>> > * Note i skipped to Scan Torsions since that
>> was all I needed amended i.e
>>
>> <FATAL_ERROR.png><SAVE_TO_LOG.log>
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io