fatal error unknown parameter in charmm parameter file line=*atoms Kings Bay Georgia

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fatal error unknown parameter in charmm parameter file line=*atoms Kings Bay, Georgia

Topics Molecular Dynamics Simulation × 1,503 Questions 2,933 Followers Follow Molecular Docking × 556 Questions 2,195 Followers Follow Autodock × 278 Questions 114 Followers Follow Apr 16, 2016 Share Facebook Twitter Cannot intersect groups using a dynamic group This operation is not allowed. As a last resort, you can send an email directly to the developers. 12.3. Thus you cannot change the timestep when one or more of these are defined.

Bond style hybrid cannot use same bond style twice Self-explanatory. All angle coeffs are not set All angle coefficients must be set in the data file or by the angle_coeff command before running a simulation. Cannot use nonperiodic boundaries with EwaldDisp For kspace style ewald/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic But how would i estimate bond dissociation energy for system with many bonds (Eg:- 1T and 2H interface in TMD's) .?

Cannot use wall in periodic dimension Self-explanatory. The bodies you have defined exceed this limit. You need to use unfix to discard the fix, change the box, then redefine a new fix. Cannot open COMB3 lib.comb3 file The COMB3 library file cannot be opened.

For example, the file says "IMPORTANT NOTE: this file contains > NBFixes between carboxylates and sodium which will only apply if the main > files containing carboxylate atom types have been All atom IDs = 0 but atom_modify id = yes Self-explanatory. Check that the path and name are correct. Cannot change_box in xz or yz for 2d simulation Self-explanatory.

Check that the path and name are correct. E.g. Cannot use delete_atoms unless atoms have IDs Your atoms do not have IDs, so the delete_atoms command cannot be used. Cannot use multiple fix wall commands with pair lubricate Self-explanatory.

All masses are not set For atom styles that define masses for each atom type, all masses must be set in the data file or by the mass command before running Cannot use nonperiodic boundaries with Ewald For kspace style ewald, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic being fix, compute, pair, etc, it means that you mistyped the style name or that the command is part of an optional package which was not compiled into your executable. Cannot use nonperiodic boundaries with PPPMDisp For kspace style pppm/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic

Cannot find delete_bonds group ID Group ID used in the delete_bonds command does not exist. Add your answer Question followers (6) Yasmine Moemen National Liver Institute Abhishek Tyagi Tushar Savane Indian Institute of Technology Delhi Justin Lemkul University of Maryland, Baltimore Amirah Cannot use fix box/relax with both relaxation and scaling on a tilt factor When specifying scaling on a tilt factor component, that component can not also be controlled by the barostat. Cannot use ramp in variable formula between runs This is because the ramp() function is time dependent.

Cannot use TAD unless atom map exists for NEB See atom_modify map command to set this. Following Keka Talukdar added an answer: 3 Forcefield for charcoal crystallite modelling? Cannot use package gpu neigh yes with triclinic box This is a current restriction in LAMMPS. I have to use both par_all36_prot.prm and par_all36_lipid.prm since I have both protein and membrane.

Cannot (yet) use PPPM with triclinic box and slab correction This feature is not yet supported. If you run into errors that LAMMPS doesn't catch that you think it should flag, please send an email to the developers. Check that the path and name are correct. Cannot use tris with fix srd unless overlap is set This is because triangles are connected to each other.

Cannot use delete_bonds with non-molecular system Your choice of atom style does not have bonds. You cannot (and should not!) assume that everything has a canonical value. Following Mood Mohan added an answer: 5 How can I convert OPLS-AA force field parameters to CHARMM force field parameters? Bond atom missing in delete_bonds The delete_bonds command cannot find one or more atoms in a particular bond on a particular processor.

I find CHARMMC35r has been testified very well for PEG by the following literature. Bond atoms missing on proc %d at step %ld The 2nd atom needed to compute a particular bond is missing on this processor. I have read the tutorial file. if you have further questions let me know.

The bond style used in the bond_coeff command or read from a restart file is not recognized. Cannot use fix npt and fix deform on same component of stress tensor This would be changing the same box dimension twice. Check that the path and name are correct. Your simulation will run fine.

Errors 12.1. Cannot (yet) use respa with Kokkos Self-explanatory. Angle_coeff command when no angles allowed The chosen atom style does not allow for angles to be defined. Bond style quartic cannot be used with atom style template This bond style can change the bond topology which is not allowed with this atom style.

This is only allowed if the command documentation says it is. Cannot open SNAP coefficient file %s The specified SNAP coefficient file cannot be opened. Thanks a lot! Reporting bugs If you are confident that you have found a bug in LAMMPS, follow these steps.

Assigning ellipsoid parameters to non-ellipsoid atom Self-explanatory. Check that the path and name are correct. Atomfile variable could not read values Check the file assigned to the variable. Packages 5.

Cannot use write_restart nfile without % in restart file name Self-explanatory. Bias compute does not calculate a velocity bias The specified compute must compute a bias for temperature. Cannot open fix rigid/small infile %s The specified file cannot be opened. Can only use TAD with 1-processor replicas for NEB This is current restriction for NEB as implemented in LAMMPS.

Cannot set quaternion for atom that has none Self-explanatory. All mol IDs should be set for fix gcmc group atoms The molecule flag is on, yet not all molecule ids in the fix group have been set to non-zero positive Introduction 2. Following Justin Lemkul added an answer: 17 How to do Constrain Minimization of Metallic Ions in Protein?

Cannot open EIM potential file %s The specified EIM potential file cannot be opened. Error & warning messages 12.4.