Error with GROMACS in topology file

Satyen Dhamankar

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Aug 20, 2021, 5:26:21 PM8/20/21

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I see that VOTCA is running the following command:
gmx_196 grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro

And I am getting the following error:
Molecule type PNM contains no atoms

This is my topol.top file:

[ defaults ]

; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ

1 1 no 0.0 0.0

[ atomtypes ]

; type mass charge ptype sigma epsilon

TB 29.04 0.000 A 0.0000 1.0000

TA 43.00 0.000 A 0.0000 1.0000

TI 43.00 0.000 A 0.0000 1.0000

TW 18.01 0.000 A 0.0000 1.0000

[ moleculetypes ]

; Name nrexcel

PNM 3

WT 1

[ atoms ]

; nr type resnr residue atom cgnr charge mass typeB chargeB massB

1 TB 1 PNM BB 1 0 29.04

2 TA 1 PNM BA 1 0 43.00

3 TI 1 PNM BI 1 0 43.00

4 TW 1 WT BW 1 0 18.01

[ bonds ]

;ai aj funct c0 c1 c2 c3

1 2 8 1 1.0

2 3 8 1 1.0

[ angles ]

;ai aj ak funct c0 c1 c2

1 2 3 8 1 1.0

[ molecules ]

;

PNM 1

WT 4046

I don’t understand what is causing this error. I have written similar types of topol.top files, and it seems to be working just fine.

For completeness sake, this is my conf.gro file:

what a nice title

4049

1PNM BB 1 2.229 1.514 4.238

1PNM BA 2 2.272 1.286 4.235

1PNM BI 3 2.194 1.048 4.125

2WT BW 4 2.276 1.580 1.676

3WT BW 5 0.119 0.703 0.277

4WT BW 6 1.682 0.128 4.229

5WT BW 7 4.889 2.252 2.343

.

4045WT BW 4047 1.332 2.041 1.148

4046WT BW 4048 0.125 1.348 4.089

4047WT BW 4049 0.839 1.673 3.898

4.98674 4.98674 4.98674 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

I would appreciate any advice you have for me!

Christoph Junghans

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Aug 20, 2021, 5:33:05 PM8/20/21

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On Fri, Aug 20, 2021 at 3:26 PM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> I see that VOTCA is running the following command:
> gmx_196 grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro
>
> And I am getting the following error:
> Molecule type PNM contains no atoms
>
> This is my topol.top file:
>
> [ defaults ]
>
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>
> 1 1 no 0.0 0.0
>
> [ atomtypes ]
>
> ; type mass charge ptype sigma epsilon
>
> TB 29.04 0.000 A 0.0000 1.0000
>
> TA 43.00 0.000 A 0.0000 1.0000
>
> TI 43.00 0.000 A 0.0000 1.0000
>
> TW 18.01 0.000 A 0.0000 1.0000
>
> [ moleculetypes ]

More a question for the gromacs mailing list, but I believe this
needs two [ moleculetype ] sections instead, see
https://github.com/votca/csg-tutorials/blob/master/urea-water/ibi/topol.top#L11-L23

Christoph

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--
Christoph Junghans
Web: http://www.compphys.de

Satyen Dhamankar

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Aug 20, 2021, 6:08:06 PM8/20/21

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You are right, Christoph. I did end up catching that error... However, I am now facing an issue with energygroups.

PNM in energygrp-table is not an energy group

This is my mdp file:

```

; RUN CONTROL PARAMETERS

integrator = sd

; Start time and timestep in ps

tinit = 0

dt = 0.004

nsteps = 1000000

; For exact run continuation or redoing part of a run

init_step = 0

; mode for center of mass motion removal

comm-mode = Linear

; number of steps for center of mass motion removal

nstcomm = 1

; group(s) for center of mass motion removal

comm-grps =

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and fo_ces (f)

nstxout = 0

nstvout = 0

nstfout = 0

; Output frequency for energies to log file and energy file

nstlog = 0

nstenergy = 5000

; Output frequency and precision for xtc file

nstxout-compressed = 100

compressed-x-precision = 1000

; Selection of energy groups

energygrps = WT PNM_&_BB PNM_&_BA PNM_&_BI

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist = 5

; ns algorithm (simple or grid)

ns-type = Grid

; Periodic boundary conditions: xyz, no, xy

pbc = xyz

periodic_molecules = no

; nblist cut-off

rlist = 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = User

rcoulomb-switch = 0

rcoulomb = 1.4

; Relative dielectric constant for the medium and the reaction field

epsilon_r = 1

epsilon_rf = 80

; Method for doing Van der Waals

vdw-type = User

; cut-off lengths

rvdw-switch = 0

rvdw = 1.4

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = EnerPres

; Extension of the potential lookup tables beyond the cut-off

table-extension = 1

; Seperate tables between energy group pairs

Set energygrps = PNM WT

energygrp_table = PNM WT WT WT

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

; FFT grid size, when a value is 0 fourierspacing will be used

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

; EWALD/PME/PPPM parameters

pme_order = 4

ewald_rtol = 1e-05

ewald_geometry = 3d

epsilon_surface = 0

; IMPLICIT SOLVENT ALGORITHM

implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

gb_algorithm = Still

; Frequency of calculating the Born radii inside rlist

nstgbradii = 1

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

rgbradii = 2

; Dielectric coefficient of the implicit solvent

gb_epsilon_solvent = 80

; Salt concentration in M for Generalized Born models

gb_saltconc = 0

; Scaling factors used in the OBC GB model. Default values are OBC(II)

gb_obc_alpha = 1

gb_obc_beta = 0.8

gb_obc_gamma = 4.85

; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA

; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.

sa_surface_tension = 2.092

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

Tcoupl = no

; Groups to couple separately

tc-grps = System

; Time constant (ps) and reference temperature (K)

tau_t = 0.2

ref_t = 330

; Pressure coupling

Pcoupl = no

Pcoupltype = isotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Scaling of reference coordinates, No, All or COM

refcoord_scaling = No

; GENERATE VELOCITIES FOR STARTUP RUN

gen-vel = no

; OPTIONS FOR BONDS

constraints = none

cutoff-scheme = Group

```

I was having trouble getting PNM as part of the energy group, so I added set energygrps to it, but it still doesnt seem to be working…

Christoph Junghans

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Aug 20, 2021, 7:41:04 PM8/20/21

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On Fri, Aug 20, 2021, 16:08 Satyen Dhamankar <saty...@gmail.com> wrote:

You are right, Christoph. I did end up catching that error... However, I am now facing an issue with energygroups.
PNM in energygrp-table is not an energy group

Did you run make_index to create all these energy groups?

Christoph

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/7c13568f-5698-4956-a6f0-d3199e5b63e9n%40googlegroups.com.

Satyen Dhamankar

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Aug 20, 2021, 11:29:27 PM8/20/21

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Yes, I had to take some time understanding GROMACS functionality to get it all working.

Thank you for the advice!

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