[gmx-users] Citrate parameters
Pandya, Akash
akash.pandya.15 at ucl.ac.uk
Fri Apr 12 17:38:46 CEST 2019
Sorry but I don't quite understand where the duplicates come from? I've pasted my itp file below:
[ defaults ]
1 2 yes 1.0 1.0
[ atomtypes ]
OC 8 15.9999 -0.760 A 0.302906 0.50208
CC 6 12.0110 0.620 A 0.356359 0.29288
HA 1 1.0080 0.090 A 0.235197 0.09205
CT2 6 12.0110 -0.180 A 0.387541 0.23012
CT 6 12.0110 -0.070 A 0.405359 0.08368
OH1 8 15.9999 -0.540 A 0.315378 0.63639
H 1 1.0080 0.310 A 0.040001 0.19623
[ bondtypes ]
CC OC 1 0.126 439320.0
CC CT2 1 0.152 167360.0
CT2 HA 1 0.111 258571.2
OH1 H 1 0.096 456056.0
CT CC 1 0.152 167360.0
CT2 CT 1 0.150 186188.0
CT OH1 1 0.142 358150.4
[ angletypes ]
OC CC OC 5 124.00 836.80 0.2225 58576.000
OC CC CT2 5 118.00 334.72 0.2388 41840.000
CC CT2 HA 5 109.50 276.14 0.2163 25104.000
HA CT2 HA 5 109.00 297.06 0.1802 4518.720
CT CC OC 5 118.00 334.72 0.2388 41840.000
CT2 CT CC 5 108.00 435.14 0.0000 0.000
CT2 CT CT2 5 113.60 488.27 0.2561 9338.688
HA CT2 CT 5 110.10 279.74 0.2179 18853.104
CC CT2 CT 5 108.00 435.14 0.0000 0.000
CT2 CT OH1 5 110.10 633.46 0.0000 0.000
OH1 CT CC 5 110.10 633.46 0.0000 0.000
CT OH1 H 5 106.00 481.16 0.0000 0.000
[ dihedraltypes ]
HA CT2 CC OC 9 180.00 0.2092 6
CT CT2 CC OC 9 180.00 0.2092 6
CT2 CT CT2 CC 9 0.00 4.0000 3
OH1 CT CT2 CC 9 0.00 0.8368 3
OH1 CT CT2 HA 9 0.00 0.8368 3
CC CT CT2 CC 9 0.00 0.8368 3
CC CT CT2 HA 9 0.00 0.8368 3
CT2 CT CT2 HA 9 0.00 0.8368 3
OH1 CT CC OC 9 0.00 1.2000 2
CT2 CT CC OC 9 180.00 0.2092 6
CC CT OH1 H 9 0.00 0.2092 1
CT2 CT OH1 H 9 0.00 0.5858 3
CC CT2 OC OC 2 0.00 803.328
CC CT OC OC 2 0.00 803.328
[ moleculetype ]
CIT 3
[ atoms ]
1 CC 1 CIT C 1 0.620 12.011
2 CT2 1 CIT C 2 -0.180 12.011
3 CT 1 CIT C 3 -0.070 12.011
4 CC 1 CIT C 4 0.620 12.011
5 CT2 1 CIT C 5 -0.180 12.011
6 CC 1 CIT C 6 0.620 12.011
7 OC 1 CIT O 7 -0.760 15.999
8 OC 1 CIT O 8 -0.760 15.999
9 OC 1 CIT O 9 -0.760 15.999
10 OC 1 CIT O 10 -0.760 15.999
11 OC 1 CIT O 11 -0.760 15.999
12 OC 1 CIT O 12 -0.760 15.999
13 OH1 1 CIT O 13 -0.540 15.999
14 HA 1 CIT H 14 0.090 1.008
15 HA 1 CIT H 15 0.090 1.008
16 HA 1 CIT H 16 0.090 1.008
17 HA 1 CIT H 17 0.090 1.008
18 H 1 CIT H 18 0.310 1.008
[ bonds ]
1 8 1
1 7 1
1 2 1
2 15 1
2 14 1
2 3 1
3 13 1
3 5 1
3 4 1
4 10 1
4 9 1
5 17 1
5 16 1
5 6 1
6 12 1
6 11 1
13 18 1
[ angles ]
8 1 7 5
8 1 2 5
7 1 2 5
1 2 15 5
15 2 14 5
15 2 3 5
1 2 14 5
14 2 3 5
1 2 3 5
2 3 13 5
13 3 5 5
13 3 4 5
2 3 5 5
5 3 4 5
2 3 4 5
3 4 10 5
10 4 9 5
3 4 9 5
3 5 17 5
17 5 16 5
17 5 6 5
3 5 16 5
16 5 6 5
3 5 6 5
5 6 12 5
12 6 11 5
5 6 11 5
3 13 18 5
[ exclusions ]
18 9 10
[ pairs ]
10 18 2 0.3 -0.760 0.310 0.17145 0.310857
9 18 2 0.3 -0.760 0.310 0.17145 0.310857
[ dihedrals ]
8 1 2 15 9
7 1 2 15 9
8 1 2 14 9
7 1 2 14 9
8 1 2 3 9
7 1 2 3 9
1 2 3 13 9
15 2 3 13 9
14 2 3 13 9
1 2 3 5 9
15 2 3 5 9
14 2 3 5 9
1 2 3 4 9
15 2 3 4 9
14 2 3 4 9
2 3 13 18 9
5 3 13 18 9
4 3 13 18 9
2 3 5 17 9
13 3 5 17 9
4 3 5 17 9
2 3 5 16 9
13 3 5 16 9
4 3 5 16 9
2 3 5 6 9
13 3 5 6 9
4 3 5 6 9
2 3 4 10 9
13 3 4 10 9
5 3 4 10 9
2 3 4 9 9
13 3 4 9 9
5 3 4 9 9
3 5 6 12 9
17 5 6 12 9
16 5 6 12 9
3 5 6 11 9
17 5 6 11 9
16 5 6 11 9
[ dihedrals ]
1 2 7 8 2
4 3 9 10 2
6 5 11 12 2
#ifdef POSRES_CITMolecule
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
11 1 1000 1000 1000
12 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
#endif
-----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 Justin Lemkul
Sent: 12 April 2019 16:14
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Citrate parameters
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
> 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%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597905747&sdata=oxvEKXN67Oq%2B2F2Wm4WQ0uPCtOZxTVsn%2Fv9hiF%2FGeCI%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
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g
> romacs.org%2FDocumentation%2FErrors&data=02%7C01%7Cakash.pandya.15
> %40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9
> 210a11d9a5c2%7C0%7C0%7C636906788597905747&sdata=WGY4ht%2BgVmeJ3bJX
> YAg5Y7ciNSUk3MhMwkbnSnob%2F0I%3D&reserved=0
>
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Justin A. Lemkul, Ph.D.
Assistant Professor
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