[obasekia]

I tried to run a minimization for a protein of interest and i get this error coordinates are too close . I dont Know if it is a problem with my pdb or my input file for minimization. i tried to upload the log file but i can’t seem to locate how to do so on the forum. so i copied and pasted

 

Read_Ctrl_Restraints> Parameters of Restraint
numfunc = 2
function1 = POSI
direction = ALL
constant = 1.0
select_index = 1
reference =
exponent = 2
exponent_dist =
weight_dist =
function2 = POSI
direction = ALL
constant = 0.1
select_index = 2
reference =
exponent = 2
exponent_dist =
weight_dist =
pressure_position = NO
pressure_rmsd = NO

Read_Ctrl_Fitting_MD> Parameters of Fitting
fitting method = TR+ROT
fitting atom = group1
mass_weight = no

[STEP2] Setup MPI

Setup_Mpi_Md> Summary of Setup MPI
number of MPI processes = 4
number of OpenMP threads = 1
total number of CPU cores = 4

[STEP3] Set Relevant Variables and Structures

Input_Top> Summary of Topfile
num_atom_class = 455 num_resi_type = 1904

Input_Par> Summary of Parfile
num_bonds = 1225 num_angles = 4010
num_dihedrals = 10945 num_impropers = 271
num_atom_cls = 455 num_nbfix = 74
num_cmap_terms = 6

Merge_Top> WARNING: RESI: Multiple definition: “MGU1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MGU2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CO2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “THFI” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “THMI” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “THFA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “THAO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “RNUS” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NUCL” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PPH1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BMPH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BMPD” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BDFP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BDFD” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EP_2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “IP_2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BTE2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “13DB” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “13DP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DMB1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DMP1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DMP2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CROT” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PACP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MECH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “TMCH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “FRET” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “RTOL” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “RTAL” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “RTAC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PRAC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PROL” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PRAL” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “SCH1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “SCH2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “SCH3” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ACET” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PROA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “GUAN” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MGUA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “GLYN” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MAMM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EAMM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ACEH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MEOH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “METO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ETOH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ETO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PRO2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “FORM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ACEM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NMA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MESH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MES1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ETSH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ES1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DMDS” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DEDS” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EMS” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “IMIA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MIMI” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EIMI” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “IMIM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EIMM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BENZ” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EBEN” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PHEN” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EPHE” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PHEO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “INDO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “EIND” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PDIP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “OCOH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “C3” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CGU” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CME” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CGUP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NIC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NICH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PPI1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PPI2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “AMP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ADP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ATP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “5DP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NAD” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NADH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NADP” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NDPH” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BUG” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CHL1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CHNS” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CHM1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MAS” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ETAC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MPRO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MP_1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MP_2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MSO4” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BUTA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PENT” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “HEXA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ETHE” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PRPE” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BTE1” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “BTE2” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DIPE” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “DIHE” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NC4” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “NC5” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “CHOL” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ACHO” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “PC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “GPC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “TEA” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “ETAM” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “GLYC” : will be ignored.
Merge_Top> WARNING: RESI: Multiple definition: “MBUT” : will be ignored.
Input_Str> Summary of Top information
num_atom_class = 575 num_resi_type = 4922

Input_Str> Summary of Par information
num_bonds = 1490 num_angles = 5212
num_dihedrals = 15439 num_impropers = 349
num_atom_cls = 575 num_nbfix = 111
num_cmap_terms = 24

Read_Psf> Summary of Psffile
psftype = xplor
num_atoms = 222872 num_bonds = 222497
num_angles = 87966 num_dihedrals = 24588
num_impropers = 1653 num_cmap_terms = 603
num_HB_donors = 0 num_HB_acceptors= 0
num_NB_exclusion= 0 num_groups = 0
total_charge = 0.000

Check_Pdb> 6-column residue sequence number

Read_Pdb> Summary of Data in PDB file
num_atoms = 222872

Define_Molecule> Summary of molecules
num_atoms = 222872 num_bonds = 222497
num_angles = 87966 num_dihedrals = 24588
num_impropers = 1653 num_cmap_terms = 603
num_residues = 72102 num_molecules = 71498
num_segments = 3 num_deg_freedom = 668616
total_charge = 0.000

Setup_Structure_Check> Setup for checking the ring size and chirality errors of proteins and DNA/RNA
num_ring_grps = 51 num_chiral_grps = 645

Setup_Boundary_Cell> Set Variables for Boundary Condition
domains (x,y,z) = 2 2 1
ncells (x,y,z) = 16 16 17

Select_kernel>
Pairlist = GENERIC
Nonbond = GENERIC

WARNING: too small distances: 7 1 0.07770
WARNING: too small distances: 19 20 0.15220
WARNING: too small distances: 9180 9189 0.21172
WARNING: too small distances: 9192 9232 0.13627
WARNING: too small distances: 9192 9233 0.13627
WARNING: too small distances: 9192 9174 0.21265
WARNING: too small distances: 9193 9231 0.08660
WARNING: too small distances: 9193 9172 0.10523
WARNING: too small distances: 9193 9194 0.16523
WARNING: too small distances: 9193 9176 0.09651
WARNING: too small distances: 9197 9206 0.21281
WARNING: too small distances: 9198 9227 0.15974
WARNING: too small distances: 9198 9199 0.15243
WARNING: too small distances: 9198 9203 0.08883
WARNING: too small distances: 9198 9228 0.00755
WARNING: too small distances: 9209 9184 0.23087
WARNING: too small distances: 9210 9182 0.05856
WARNING: too small distances: 9210 9186 0.08753
WARNING: too small distances: 9210 9211 0.16477
WARNING: too small distances: 9214 9223 0.21119
WARNING: too small distances: 9215 9216 0.15256
WARNING: too small distances: 9215 9220 0.08787
WARNING: too small distances: 9226 9201 0.23090
WARNING: too small distances: 9227 9199 0.05697
WARNING: too small distances: 9227 9203 0.08648
WARNING: too small distances: 9227 9228 0.16464
WARNING: too small distances: 9231 9172 0.12559
WARNING: too small distances: 9231 9194 0.24543
WARNING: too small distances: 9231 9176 0.17991
Check_Atom_Coord> coordinates are too close rank_no = 3

 

[obasekia]

I tried it again and i got an error about

WARNING: too long bond: 6200 6199 2.87516
Setup_Fitting_Spdyn> NO fitting is applied, skip
fitting method = NO

Memory allocation error rank_no = 1
Memory allocation error rank_no = 2
Memory allocation error rank_no = 3
Memory allocation error rank_no = 0

[jwjung]

The initial structure seems to be very unstable. Please try structure_check and nonb_limiter option. I’m not sure of the memory allocation error. One possibility is that the memory in your computer is not sufficient.

[obasekia]

Thanks checked my log file i can see MPI compiler = NO MPI does that mean i complied genesis without mpi?

[jwjung]

In your log, you compiled with MPI. For SPDYN, you need to compile with MPI.