[gmx-users] Citrate parameters

[Soham Sarkar]

Which force field you are using and how you made the itp of the citrate
molecule?

On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash, <akash.pandya.15 at ucl.ac.uk>
wrote:

> 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
>
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