[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&amp;data=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597905747&amp;sdata=oxvEKXN67Oq%2B2F2Wm4WQ0uPCtOZxTVsn%2Fv9hiF%2FGeCI%3D&amp;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&amp;data=02%7C01%7Cakash.pandya.15
> %40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9
> 210a11d9a5c2%7C0%7C0%7C636906788597905747&amp;sdata=WGY4ht%2BgVmeJ3bJX
> YAg5Y7ciNSUk3MhMwkbnSnob%2F0I%3D&amp;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
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thelemkullab.com&amp;data=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597905747&amp;sdata=B1%2BYyTynurYrn465N16FQfCW%2FrCvEqezzRuDIBc5%2Bo8%3D&amp;reserved=0

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

--
Gromacs Users mailing list

* Please search the archive at https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597915752&amp;sdata=RVt84Lxd0iThvqPJ0hXuRzX2PAJzA5vHpiCBNh677Ho%3D&amp;reserved=0 before posting!

* Can't post? Read https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597915752&amp;sdata=E2x8Ym8WPpUhxSBVPoSku%2FspW6EtQ8%2Fw2eDkZkTZxaE%3D&amp;reserved=0

* For (un)subscribe requests visit
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597915752&amp;sdata=JQ6GkGo%2BJBSWD2xC1CWNwLD%2FWqee%2Byszy7NeAVM82QY%3D&amp;reserved=0 or send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list