[gmx-users] Citrate parameters

[Pandya, Akash]

Hi all,

My simulation contains citrate molecules. When I try to solvate the system, I get this error. Can anybody help with this?

WARNING 1 [file CITff.itp, line 3]:
  Overriding atomtype OC


WARNING 2 [file CITff.itp, line 4]:
  Overriding atomtype CC


WARNING 3 [file CITff.itp, line 5]:
  Overriding atomtype HA


WARNING 4 [file CITff.itp, line 6]:
  Overriding atomtype CT2


WARNING 5 [file CITff.itp, line 7]:
  Overriding atomtype CT


WARNING 6 [file CITff.itp, line 8]:
  Overriding atomtype OH1


WARNING 7 [file CITff.itp, line 9]:
  Overriding atomtype H


WARNING 8 [file CITff.itp, line 13]:
  Overriding Bond parameters.

  old:                                          0.1522 167360 0.1522 167360
  new: CC     CT2 1  0.152 167360.0


WARNING 9 [file CITff.itp, line 14]:
  Overriding Bond parameters.

  old:                                          0.1111 258571 0.1111 258571
  new: CT2    HA  1  0.111 258571.2


WARNING 10 [file CITff.itp, line 23]:
  Overriding U-B parameters.

  old:                                          109.5 276.144 0.2163 25104 109.5 276.144 0.2163 25104
  new: CC   CT2    HA  5 109.50   276.14   0.2163   25104.000


WARNING 11 [file CITff.itp, line 24]:
  Overriding U-B parameters.

  old:                                          109 297.064 0.1802 4518.72 109 297.064 0.1802 4518.72
  new: HA   CT2    HA  5 109.00   297.06   0.1802    4518.720

Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_H'
Excluding 3 bonded neighbours molecule type 'CIT'
Excluding 3 bonded neighbours molecule type 'GLY'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 62703]:
  System has non-zero total charge: -46.999995
  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.



Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  1366    Protein residues
There are:    23      Other residues
There are: 56714      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 389088.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 104x104x104, spacing 0.120 0.120 0.120
Estimate for the relative computational load of the PME mesh part: 0.19
This run will generate roughly 14 Mb of data

There were 2 notes

There were 11 warnings

-------------------------------------------------------
Program:     gmx grompp, version 2016.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)

Fatal error:
Too many warnings (11).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors