[gmx-users] Citrate parameters
Pandya, Akash
akash.pandya.15 at ucl.ac.uk
Fri Apr 12 16:52:36 CEST 2019
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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