[gmx-users] Citrate parameters

[Justin Lemkul]

On 4/12/19 10:52 AM, Pandya, Akash wrote:
> Hi all,
>
> My simulation contains citrate molecules. When I try to solvate the system, I get this error. Can anybody help with this?

Your citrate topology is introducing duplicate parameters that already 
exist in the force field. In this instance, they appear to be exact 
copies (at least for the bonded parameters shown) but this is bad 
practice. Eliminate the redundancies.

-Justin

> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================