VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Sat Oct 31 2020 - 03:15:46 CDT

Did you check that the atom names in the fragment files matched the
corresponding atoms in the STR file, and that the atom names of any
overlapping atoms in the fragment files also match?

Other than that, I'm not particularly familiar with NAMD as I use GROMACS
via CHARMM-GUI

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Sat, Oct 31, 2020 at 5:45 PM Emma Wu <ewu20_at_illinois.edu> wrote:

> Hi Daniel,
> I have been trying this approach you've recommended and now I am trying to
> run the solvated molecule in NAMD. However, I currently am running into
> this issue:
>
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE 53297_wb.dcd AT STEP 1000
> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART COORDINATES
> The last position output (seq=1000) takes 0.008 seconds, 323.957 MB of
> memory in use
> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART VELOCITIES
> The last velocity output (seq=1000) takes 0.005 seconds, 323.957 MB of
> memory in use
> TCL: Running for 12500000 steps
> PRESSURE: 1000 -26365.3 -628.573 -406.464 -628.573 -26294.1 187.322
> -406.464 187.322 -26208.9
> GPRESSURE: 1000 -2800.41 -74.6814 -71.2824 -28.3342 -2448.95 309.583
> -77.8142 291.198 -2478.83
> ENERGY: 1000 28.6571 124.9912 73.4387
> 1.4656 -19458.0156 2344.5741 0.0000 0.0000
> 0.0000 -16884.8889 0.0000 -16884.8889 -16887.1558
> 0.0000 -26289.4728 -2576.0640 46537.7774
> -26289.4728 -2576.0640
>
> Info: Initial time: 48 CPUs 0.00094703 s/step 0.010961 days/ns 323.957 MB
> memory
> Info: Initial time: 48 CPUs 0.00102655 s/step 0.0118814 days/ns 323.957 MB
> memory
> ERROR: Constraint failure in RATTLE algorithm for atom 12!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
>
>
> *Here is my NAMD file:*
> ## specify pdb and psf files and the name used for output files
>
> structure 53297_wb.psf
> coordinates 53297_wb.pdb
> outputname 53297_wb
>
> # force field / parameter files are specified here
> # force field.
> paraTypeCharmm on
> parameters toppar_water_ions.mod.str
> parameters par_all36_prot.prm
> parameters LIG.analogy.par
> parameters 53297.prm
> parameters LIG.existing.par
> parameters par_all36m_prot.prm
> parameters par_all36_na.prm
> mergeCrossterms yes
> parameters par_all36_lipid.prm
> parameters par_all36_carb.prm
> parameters par_all36_cgenff.prm
> parameters toppar_water_ions_namd.str
>
> #simulation box size and center
> cellBasisVector1 52.214 0. 0.
> cellBasisVector2 0. 32.599 0.
> cellBasisVector3 0. 0 27.341
> cellOrigin -0.03979 -0.17819 0.027215
>
>
> # energy calculations parameters
> firsttimestep 0
> wrapWater on
> wrapAll on
> wrapNearest off
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 10
> cutoff 12
> pairlistdist 13.5
>
> PME on
> PMEGridSpacing 1.0
>
> rigidBonds all
> rigidTolerance 0.00000001
> rigidIterations 100
> useSettle on
>
> margin 4.0
>
>
> # temperature and pressure
> set temp 300
> temperature $temp
> langevin on
> langevinTemp $temp
> langevinDamping 1
> useGroupPressure yes
> useFlexibleCell no
> LangevinPiston on
> LangevinPistonTarget 1
> LangevinPistonPeriod 200
> LangevinPistonDecay 100
> LangevinPistonTemp $temp
>
> # output parameters
> outputTiming 1000
> outputEnergies 1000
> outputPressure 1000
> binaryoutput yes
>
> DCDfreq 1000
> xstfreq 1000
> DCDUnitCell yes
>
> restartfreq 1000
> restartsave no
> binaryrestart yes
>
> timestep 1.0
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> # the number of time steps to minimize and then simulate
> minimize 1000
> run 12500000
>
> I am not sure how to approach this issue. I essentially took the str file
> from paramchem and copied and pasted the parameters from the fragments to
> the file. Then I generated the psf and pdb using fttk from that and
> solvated them for the inputs for the simulation. Thank you so much in
> advance for all and any help!
>
> Best,
> Emma
>
> On Thu, Oct 15, 2020 at 1:05 AM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
> wrote:
>
>> What I would do is generate "template" parameters with paramchem, split
>> the .str file into the respective .rtf and .prm files for the topology and
>> parameters, respectively. And then copy paste the associated fragment
>> parameters into these files.
>>
>> When dealing with overlaps, you could compare the overlapping portions of
>> both and see if there's good agreement, and then decide which ones you'll
>> paste into the whole molecule.
>>
>> The CGenFF menu in the BuildPar tab of FFTK can generate PSF/PDB files
>> from your .str file
>>
>> *Daniel Fellner BSc(Hons)*
>> PhD Candidate
>> School of Chemical Sciences
>> University of Auckland
>> Ph +64211605326
>>
>>
>> On Thu, Oct 15, 2020 at 6:52 PM Emma Wu <ewu20_at_illinois.edu> wrote:
>>
>>> Hi all,
>>> I have a molecule that I have fragmented and parameterized each fragment
>>> using ffTK. I am now trying to combine the fragments but I am unsure how I
>>> should proceed. I have overlapping fragments that include the linker
>>> portion.
>>>
>>> Here are the things I am confused about:
>>> 1. Since I have the linker portions optimized through overlapping
>>> fragments, how would I combine that information into the pdb, psf, and par?
>>>
>>> 2. How would I get a new pdb of the full molecule from fragments pdbs
>>> that I have optimize?
>>>
>>> Thank you so much for all and any suggestions!
>>>
>>> Best,
>>> Emma
>>>
>>