[gmx-users] Citrate parameters
Pandya, Akash
akash.pandya.15 at ucl.ac.uk
Fri Apr 12 17:08:06 CEST 2019
I'm using the CHARMM27 FF and I obtained the parameters from literature.
Akash
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Soham Sarkar
Sent: 12 April 2019 16:05
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Citrate parameters
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
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FFloating_Point_Arithmetic&data=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906783645721595&sdata=mMSRKLOaTcASmbpt%2BVctQztiZY%2F6xpgswsGtQUIrI5s%3D&reserved=0
> 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
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