[gmx-users] mismatch sol.gro/topol.gro

Wed Nov 28 18:42:55 CET 2018

I am preparing (as a newcomer to gromacs) a complex of a protein with two
ligands. One is the universal GDP, the other one a diterpenoid. GROMCS2018,
CGenFF, CHARMM36.

The output of addions complains about GDP.prm (the GDP.str of CGenFF origin
had no problems for NAMD/CHARMM36) and (because of this, or not) there is a
mismatch of ion number
Fatal error:
number of coordinates in coordinate file (complex_solv.gro, 51025)
             does not match topology (topol.top, 51137).

Attached the full output. Grateful for advice
-------------- next part --------------
python cgenff_charmm2gmx.py GDP GDP_fix.mol2 GDP.str charmm36-nov2018.ff
python cgenff_charmm2gmx.py SAA SAA_fix.mol2 SAA.str charmm36-nov2018.ff

providing .itp .prm .ini.pdb, i.e., cgenff_charmm2gmx.py works also with NetworkX2.x of Debian buster, contrary to tutorial warning.

Then

gmx editconf -f gdp_ini.pdb -o gdp.gro

works well once the definition in the .mol2 file is reduced from a full path (/scratch/phpK1JFey_GDP_H.pdb) to no more than four characters (GDP and SAA), as said above.

COMPLEX 
The coordinates of the ligands were added to those for the receptor (at the end, before the dimensions of the cell), getting complex.gro.

TOPOLOGY

Two lines were inserted that say #include "gdp.itp" and #include "saa.itp" into topol.top after the position restraint file is included.

At the top of topol.top, after the parent ff (charmm36), and before any moleculetype was declered, was added

; Include ligand parameters
#include "gdp.prm"
#include "saa.prm"

Finally, "GDP   1" and "SAA  1" were added to [ molecules ] near the end of complex.gro.

BOX & SOLVATION

Command line:

  gmx editconf -f complex.gro -o complex_newbox.gro -bt dodecahedron -d 1.0

WARNING: Bad box in file complex.gro {same as abobe, when I used a cubic box}

Generated a cubic box    5.879 x    5.963 x    6.120
Read 6589 atoms
Volume: 214.546 nm^3, corresponds to roughly 96500 electrons
No velocities found
    system size :  5.879  5.963  6.120 (nm)
    diameter    :  7.020               (nm)
    center      : 32.540 44.856 32.401 (nm)
    box vectors :  5.879  5.963  6.120 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 214.55               (nm^3)
    shift       :-25.776-38.092-29.212 (nm)
new center      :  6.765  6.765  3.189 (nm)
new box vectors :  9.020  9.020  9.020 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 518.85               (nm^3)

Command line:

  gmx solvate -cp complex_newbox.gro -cs spc216.gro -p topol.top -o complex_solv.gro

Reading solute configuration
Good gRace! Old Maple Actually Chews Slate
Containing 6589 atoms in 426 residues
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues

Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

Generating solvent configuration
Will generate new solvent configuration of 5x5x4 boxes
Solvent box contains 57795 atoms in 19265 residues
Removed 7263 solvent atoms due to solvent-solvent overlap
Removed 6096 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 14812 residues
Generated solvent containing 44436 atoms in 14812 residues
Writing generated configuration to complex_solv.gro

Back Off! I just backed up complex_solv.gro to ./#complex_solv.gro.1#

Output configuration contains 51025 atoms in 15238 residues
Volume                 :     518.851 (nm^3)
Density                :     1017.19 (g/l)
Number of solvent molecules:  14812   

Processing topology
Adding line for 14812 solvent molecules with resname (SOL) to topology file (topol.top)

ADD IONS
 gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr

Command line:
  gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr

NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -1441611641

WARNING 1 [file gdp.prm, line 4]:
  Overriding Bond parameters.

  old:                                          0.1379 301248 0.1379 301248 
  new: CG2RC0   NG2R61     1   0.13790000    317984.00

WARNING 2 [file gdp.prm, line 10]:
  Overriding U-B parameters.

  old:                                          127.4 493.712 0 0 127.4 493.712 0 0 
  new: CG2RC0   CG2RC0   NG2R61     5   127.400000   502.080000   0.00000000         0.00

WARNING 3 [file gdp.prm, line 13]:
  Overriding U-B parameters.

  old:                                          117.4 267.776 0 0 117.4 267.776 0 0 
  new: CG2RC0   NG2R61     HGP1     5   120.700000   276.144000   0.00000000         0.00

ERROR 1 [file gdp.prm, line 23]:
  Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
  multiple lines. This is not supported.

ERROR 2 [file gdp.prm, line 25]:
  Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
  multiple lines. This is not supported.

ERROR 3 [file gdp.prm, line 29]:
  Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
  multiple lines. This is not supported.

ERROR 4 [file gdp.prm, line 31]:
  Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
  multiple lines. This is not supported.

Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
Excluding 3 bonded neighbours molecule type 'GDP'
Excluding 3 bonded neighbours molecule type 'SAA'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 62180]:
  System has non-zero total charge: -17.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

Fatal error:
number of coordinates in coordinate file (complex_solv.gro, 51025)
             does not match topology (topol.top, 51137)