Hello,

Yes, You are quite right, this halogen belongs to the amiloride molecule. So, if I replace it with  CH3 group or simply remove it, the errors will disappear?

In addition, charmm-gui offers a number of inp files to minimize and equilibrate (em and eq) the system, while the tutorial describes a smaller system, thus, contains less files. As I understand, I should pass through the charmm-gui inp files until the production MD step, and then combine those parameters suitable for my system (suggested with a charmm-gui md.inp) with the tutorial’s TMD section… am I right?

Thank You for Your response!

good morning all ))

we conducted all equilibration simulations for several protein systems, considering Your advice on chlorine atom (Kobayashi). However, we faced another problem on the MD simulation step. Here is a test inp file for spdyn algorithm application.

[INPUT]
topfile = ../toppar/top_all36_prot.rtf, ../toppar/top_all36_na.rtf, ../toppar/top_all36_carb.rtf, ../toppar/top_all36_lipid.rtf, ../toppar/top_all36_cgenff.rtf, ../toppar/top_interface.rtf, ../lig/lig.rtf
parfile = ../toppar/par_all36m_prot.prm, ../toppar/par_all36_na.prm, ../toppar/par_all36_carb.prm, ../toppar/par_all36_lipid.prm, ../toppar/par_all36_cgenff.prm, ../toppar/par_interface.prm, ../lig/lig.prm
strfile = ../toppar/toppar_all36_moreions.str, ../toppar/toppar_all36_nano_lig.str, ../toppar/toppar_all36_nano_lig_patch.str, ../toppar/toppar_all36_synthetic_polymer.str, ../toppar/toppar_all36_synthetic_polymer_patch.str, ../toppar/toppar_all36_polymer_solvent.str, ../toppar/toppar_water_ions.str, ../toppar/toppar_dum_noble_gases.str, ../toppar/toppar_ions_won.str, ../toppar/toppar_all36_prot_arg0.str, ../toppar/toppar_all36_prot_c36m_d_aminoacids.str, ../toppar/toppar_all36_prot_fluoro_alkanes.str, ../toppar/toppar_all36_prot_heme.str, ../toppar/toppar_all36_prot_na_combined.str, ../toppar/toppar_all36_prot_retinol.str, ../toppar/toppar_all36_prot_model.str, ../toppar/toppar_all36_prot_modify_res.str, ../toppar/toppar_all36_na_nad_ppi.str, ../toppar/toppar_all36_na_rna_modified.str, ../toppar/toppar_all36_lipid_sphingo.str, ../toppar/toppar_all36_lipid_archaeal.str, ../toppar/toppar_all36_lipid_bacterial.str, ../toppar/toppar_all36_lipid_cardiolipin.str, ../toppar/toppar_all36_lipid_cholesterol.str, ../toppar/toppar_all36_lipid_dag.str, ../toppar/toppar_all36_lipid_inositol.str, ../toppar/toppar_all36_lipid_lnp.str, ../toppar/toppar_all36_lipid_lps.str, ../toppar/toppar_all36_lipid_mycobacterial.str, ../toppar/toppar_all36_lipid_miscellaneous.str, ../toppar/toppar_all36_lipid_model.str, ../toppar/toppar_all36_lipid_prot.str, ../toppar/toppar_all36_lipid_tag.str, ../toppar/toppar_all36_lipid_yeast.str, ../toppar/toppar_all36_lipid_hmmm.str, ../toppar/toppar_all36_lipid_detergent.str, ../toppar/toppar_all36_lipid_ether.str, ../toppar/toppar_all36_carb_glycolipid.str, ../toppar/toppar_all36_carb_glycopeptide.str, ../toppar/toppar_all36_carb_imlab.str, ../toppar/toppar_all36_label_spin.str, ../toppar/toppar_all36_label_fluorophore.str

psffile = step5_input.psf # protein structure file
pdbfile = step5_input.pdb # PDB file

rstfile = step6.6_equilibration.rst # restart file

#localresfile is not assigned, as there is no corresponding restraint file from the charmm-gui

[OUTPUT]
rstfile = step7_production.rst
dcdfile = step7_production.dcd

[ENERGY]
forcefield = CHARMM # [CHARMM]
electrostatic = PME # [CUTOFF,PME]
switchdist = 10.0 # switch distance
cutoffdist = 12.0 # cutoff distance
pairlistdist = 13.5 # pair-list distance
vdw_force_switch = YES
pme_nspline = 4

[DYNAMICS]
integrator = VVER # [LEAP,VVER]
timestep = 0.002 # timestep (ps)
nsteps = 50000 # number of MD steps
crdout_period = 50000
eneout_period = 1000 # energy output period
rstout_period = 5000
nbupdate_period = 10

[CONSTRAINTS]
rigid_bond = YES # constraints all bonds involving hydrogen
fast_water = YES
shake_tolerance = 1.0D-10
water_model = NONE

[ENSEMBLE]
ensemble = NPT # [NVE,NVT,NPT]
tpcontrol = NHC # thermostat and barostat
temperature = 323.15
pressure = 1.0 # atm
gamma_t = 1.0
gamma_p = 0.05
isotropy = SEMI-ISO

[BOUNDARY]
type = PBC # [PBC]

and here is an example of the error string:

Setup_Enefunc_Angl_Constraint> Some angle paremeters are missing. rank_no = 31

taking into account the fact, that all files were prepared into automatic mode by charmm-gui server, I suppose, I made some mistakes by myself

thank You!

Great, it works!

This is strange, that charmm-gui output files contain these turned on controversial options in a single section.

Is it a correct suggestion, that rmsd analysis could be provided based on any heavy atoms (ligand, nucleic acid residues), but not only protein heavy atoms? And as I understood, if I work with a dimer protein with a bound substrate and I’m interested in a substrate directed/targeted motion, I have to declare two groups : group1 = segid: PROA & segid:PROB & get   and   group2: mlname: LIG & het

Am I right?

Thank You

Dear <span class=”bbp-author-name”>ckobayashi,</span>

Your advices have been definitely useful and I complete several simulations and analyzed them, observing the trends we expected. However, I prepared another very similar model with a charmm-gui and followed the same steps  and used the same inp files (slightly modified parameter files from the CHARMM output for Genesis). I passed all minimization and equilibration stages, being sure that I’ll have no problems with the production run, but I was wrong – the log file ended with the line:

Compute_Shake> SHAKE algorithm failed to converge: indexes

Neither repeatable equilibration steps, nor production input file modification (integrator, iteration step value, temperature) gave nothing… I inspected the manual and forum, but not thoroughly enough (I missed a clash-check and ring penetration section). From these I  used Chimera to identify the problem regions – two pairs of lipids from the opposite sides of the membrane intertwined suddenly, when the PBC protocol was applied to the system.

As I had all the files from CHARMM (psf, topprams, inp) I decided to change just coordinates from the last frame of the final equilibration dcd trajectory (crd_convert -> pdb file). The resulting pdb file structure  was compared with the initial input pdb file from the CHARMM output.  I did everything clear and tested the novel system with one of the equilibration steps.

But the production run crashed again. Do You have any suggestions, what should I do? Thank You!