VMD-L Mailing List

From: Emma Wu (ewu20_at_illinois.edu)
Date: Fri Oct 30 2020 - 23:47:35 CDT

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
>>
>