[gmx-users] Citrate parameters
Justin Lemkul
jalemkul at vt.edu
Fri Apr 12 17:58:52 CEST 2019
On 4/12/19 11:57 AM, Pandya, Akash wrote:
> How would I find out if there are duplicates or not?
grompp has told you what it is finding as duplicates. You need to look
into the parent force field files and compare the values you are
supplying vs. what are in the existing force field, particularly for the
atom types. grompp has already told you the existing (force field) and
new (your topology) values.
-Justin
> 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 Mark Abraham
> Sent: 12 April 2019 16:47
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Citrate parameters
>
> Hi,
>
> It seems that all/most things before the [moleculetype] definition duplicates the standard contents of the forcefield, as you can see from the contents of the itp file and the original warnings you mentioned.
> Unfortunately you now have the problem of determining whether all of it is duplication, or only some of it.
>
> Mark
>
> On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, <akash.pandya.15 at ucl.ac.uk>
> wrote:
>
>> 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.g
>> romacs.org%2FDocumentation%2FFloating_Point_Arithmetic&data=02%7C0
>> 1%7Cakash.pandya.15%40ucl.ac.uk%7Cab3034e7ecb04f59f69408d6bf5e45aa%7C1
>> faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906808956868796&sdata
>> =4J2OHbme3h%2B0cWCbc9tWTO08P5ADEyJwdEuu3FiZw7U%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%7C1faf88fea9984c5b93
>>> c9
>>> 210a11d9a5c2%7C0%7C0%7C636906788597905747&sdata=WGY4ht%2BgVmeJ3b
>>> JX
>>> YAg5Y7ciNSUk3MhMwkbnSnob%2F0I%3D&reserved=0
>>>
>> --
>> ==================================================
>>
>> 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
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==================================================
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