Ligand Parameters

GROMACS version: 5.1.4
GROMACS modification: No

Respected Community Members, I have two questions and both of them are related to ligand parameterization. Hence, I will be writing both of them in this same thread. I am working on protein-ligand complex simulation using gromacs version 5.1.4. I have performed molecular docking using Autodock 4.2 and obtained the docked protein-ligand complex for MD simulation analysis. My ligand is a cholesterol molecule. I have made the ligand topolgy using the CGenFF Server. The .str file that I obtained from the server states that it has to be used with CGenFF version 4.5.

  • Toppar stream file generated by
  • CHARMM General Force Field (CGenFF) program version 2.5
  • For use with CGenFF version 4.5

Now, I also downloaded the latest charmm36-jul2021.ff.tgz port which is having Cgenff version 4.6 as mentioned in the forcefield.doc file .

Now while running the cgenff_charmm2gmx.py script I got the following error:

WARNING: CGenFF versions are not equivalent!

However, the conversion was successful and I got the 4 files namely .itp, .top, .pdb, and .prm for the ligand. I have used these files to build the complex and then I was able to run the simulation successfully. I did not get any error messages while setting the simulation and running it up. I am just worried because of the WARNING message that I received while running the cgenff_charmm2gmx.py script. I understand that some sort consistency is required to be maintained between the different versions of CGenFF. I just wanted to ask whether there is any need to be concerned regarding this or is it just fine.

My second doubt is that the ligand that I am working on is cholesterol. As I explained earlier I generated the topology of cholesterol using the CGenFF Server. After conversion of the .str file using the cgenff_charmm2gmx.py, I got the .itp file which shows the charges on the atoms of the cholesterol molecule. A portion of that .itp file is copied and pasted below:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 UNK rtp UNK q qsum
1 CG3RC1 1 UNK C1 1 0.000 12.011 ;
2 CG3RC1 1 UNK C2 2 -0.089 12.011 ;
3 CG311 1 UNK C3 3 -0.094 12.011 ;
4 CG311 1 UNK C4 4 -0.088 12.011 ;
5 CG3C51 1 UNK C5 5 -0.091 12.011 ;
6 CG321 1 UNK C6 6 -0.184 12.011 ;
7 CG301 1 UNK C7 7 -0.004 12.011 ;
8 CG3C52 1 UNK C8 8 -0.186 12.011 ;
9 CG321 1 UNK C9 9 -0.180 12.011 ;
10 CG3C52 1 UNK C10 10 -0.180 12.011 ;
11 CG321 1 UNK C11 11 -0.179 12.011 ;
12 CG331 1 UNK C12 12 -0.271 12.011 ;
13 CG2D1 1 UNK C13 13 -0.002 12.011 ;
14 CG321 1 UNK C14 14 -0.181 12.011 ;
15 CG2D1 1 UNK C15 15 -0.152 12.011 ;
16 CG331 1 UNK C16 16 -0.270 12.011 ;
17 CG321 1 UNK C17 17 -0.181 12.011 ;
18 CG321 1 UNK C18 18 -0.180 12.011 ;
19 CG311 1 UNK C19 19 0.139 12.011 ;
20 CG311 1 UNK C20 20 -0.087 12.011 ;
21 CG331 1 UNK C21 21 -0.271 12.011 ;
22 CG321 1 UNK C22 22 -0.180 12.011 ;
23 CG321 1 UNK C23 23 -0.172 12.011 ;
24 CG321 1 UNK C24 24 -0.179 12.011 ;
25 CG311 1 UNK C25 25 -0.081 12.011 ;
26 CG331 1 UNK C26 26 -0.269 12.011 ;
27 CG331 1 UNK C27 27 -0.269 12.011 ;
28 OG311 1 UNK O 28 -0.648 15.999 ;
29 HGP1 1 UNK H1 29 0.419 1.008 ;
30 HGA1 1 UNK H2 30 0.090 1.008 ;
31 HGA1 1 UNK H3 31 0.090 1.008 ;
32 HGA1 1 UNK H4 32 0.090 1.008 ;
33 HGA1 1 UNK H5 33 0.090 1.008 ;
34 HGA2 1 UNK H6 34 0.090 1.008 ;
35 HGA2 1 UNK H7 35 0.090 1.008 ;
36 HGA2 1 UNK H8 36 0.090 1.008 ;
37 HGA2 1 UNK H9 37 0.090 1.008 ;
38 HGA2 1 UNK H10 38 0.090 1.008 ;
39 HGA2 1 UNK H11 39 0.090 1.008 ;
40 HGA2 1 UNK H12 40 0.090 1.008 ;
41 HGA2 1 UNK H13 41 0.090 1.008 ;
42 HGA2 1 UNK H14 42 0.090 1.008 ;
43 HGA2 1 UNK H15 43 0.090 1.008 ;
44 HGA3 1 UNK H16 44 0.090 1.008 ;
45 HGA3 1 UNK H17 45 0.090 1.008 ;
46 HGA3 1 UNK H18 46 0.090 1.008 ;
47 HGA2 1 UNK H19 47 0.090 1.008 ;
48 HGA2 1 UNK H20 48 0.090 1.008 ;
49 HGA4 1 UNK H21 49 0.150 1.008 ;
50 HGA3 1 UNK H22 50 0.090 1.008 ;
51 HGA3 1 UNK H23 51 0.090 1.008 ;
52 HGA3 1 UNK H24 52 0.090 1.008 ;
53 HGA2 1 UNK H25 53 0.090 1.008 ;
54 HGA2 1 UNK H26 54 0.090 1.008 ;
55 HGA2 1 UNK H27 55 0.090 1.008 ;
56 HGA2 1 UNK H28 56 0.090 1.008 ;
57 HGA1 1 UNK H29 57 0.090 1.008 ;
58 HGA1 1 UNK H30 58 0.090 1.008 ;
59 HGA3 1 UNK H31 59 0.090 1.008 ;
60 HGA3 1 UNK H32 60 0.090 1.008 ;
61 HGA3 1 UNK H33 61 0.090 1.008 ;
62 HGA2 1 UNK H34 62 0.090 1.008 ;
63 HGA2 1 UNK H35 63 0.090 1.008 ;
64 HGA2 1 UNK H36 64 0.090 1.008 ;
65 HGA2 1 UNK H37 65 0.090 1.008 ;
66 HGA2 1 UNK H38 66 0.090 1.008 ;
67 HGA2 1 UNK H39 67 0.090 1.008 ;
68 HGA1 1 UNK H40 68 0.090 1.008 ;
69 HGA3 1 UNK H41 69 0.090 1.008 ;
70 HGA3 1 UNK H42 70 0.090 1.008 ;
71 HGA3 1 UNK H43 71 0.090 1.008 ;
72 HGA3 1 UNK H44 72 0.090 1.008 ;
73 HGA3 1 UNK H45 73 0.090 1.008 ;
74 HGA3 1 UNK H46 74 0.090 1.008 ;

Later, I came to realize that the Charmm36 forcefield already has the parameters for cholesterol stored in cgenff.rtp file in its directory. A relevant portion of that file is copied and pasted below:
[ CLOL ]
; C27H46O, cholesterol (name to avoid conflict with choline)
[ atoms ]
C3 CG311 0.1400 1
O3 OG311 -0.6500 1
H3’ HGP1 0.4200 1
H3 HGA1 0.0900 1
C4 CG321 -0.1800 2
H4A HGA2 0.0900 2
H4B HGA2 0.0900 2
C5 CG2D1 0.0000 3
C6 CG2D1 -0.1500 3
H6 HGA4 0.1500 3
C7 CG321 -0.1800 4
H7A HGA2 0.0900 4
H7B HGA2 0.0900 4
C8 CG311 -0.0900 5
H8 HGA1 0.0900 5
C14 CG3RC1 -0.0900 6
H14 HGA1 0.0900 6
C15 CG3C52 -0.1800 7
H15A HGA2 0.0900 7
H15B HGA2 0.0900 7
C16 CG3C52 -0.1800 8
H16A HGA2 0.0900 8
H16B HGA2 0.0900 8
C17 CG3C51 -0.0900 9
H17 HGA1 0.0900 9
C13 CG3RC1 0.0000 10
C18 CG331 -0.2700 11
H18A HGA3 0.0900 11
H18B HGA3 0.0900 11
H18C HGA3 0.0900 11
C12 CG321 -0.1800 12
H12A HGA2 0.0900 12
H12B HGA2 0.0900 12
C11 CG321 -0.1800 13
H11A HGA2 0.0900 13
H11B HGA2 0.0900 13
C9 CG311 -0.0900 14
H9 HGA1 0.0900 14
C10 CG301 0.0000 15
C19 CG331 -0.2700 16
H19A HGA3 0.0900 16
H19B HGA3 0.0900 16
H19C HGA3 0.0900 16
C1 CG321 -0.1800 17
H1A HGA2 0.0900 17
H1B HGA2 0.0900 17
C2 CG321 -0.1800 18
H2A HGA2 0.0900 18
H2B HGA2 0.0900 18
C20 CG311 -0.0900 19
H20 HGA1 0.0900 19
C21 CG331 -0.2700 20
H21A HGA3 0.0900 20
H21B HGA3 0.0900 20
H21C HGA3 0.0900 20
C22 CG321 -0.1800 21
H22A HGA2 0.0900 21
H22B HGA2 0.0900 21
C23 CG321 -0.1800 22
H23A HGA2 0.0900 22
H23B HGA2 0.0900 22
C24 CG321 -0.1800 23
H24A HGA2 0.0900 23
H24B HGA2 0.0900 23
C25 CG311 -0.0900 24
H25 HGA1 0.0900 24
C26 CG331 -0.2700 25
H26A HGA3 0.0900 25
H26B HGA3 0.0900 25
H26C HGA3 0.0900 25
C27 CG331 -0.2700 26
H27A HGA3 0.0900 26
H27B HGA3 0.0900 26
H27C HGA3 0.0900 26

Now my question is that I am finding the difference in the atom and residue numbering between the two files. For example, C1 in .itp file is CG3RC1 atom while in the cgenff.rtp file C1 happens to be CG321 atom. The naming of the atoms are however consistent between the two files. If I have to compare the charges for any atom between the two files (.itp generated by CGenFF and the parameters for cholesterol in cgenff.rtp in the forcefield directory), I have to manually search for the atom name since the numbering is different. The charges are more or less same for the atoms between the two files. Now, is this numbering discrepancy going to affect my simulation in any way. Should I be concerned over the apparent discrepancy. I am new user of Gromacs so please excuse me if my doubts seem very trivial. I hope some one can clear these two doubts.
Thanks for reading this post.

Rename your residue CHL1 and make sure its atom naming is consistent. CHL1 is the more optimized version of cholesterol developed alongside the rest of the lipid parameters. CLOL is a CGenFF version of it that can be used but is present in the force field more as a training molecule for the CGenFF program.

Thanks Dr. Lemkul for replying to my question. So do you mean to say instead of UNK I should name my cholesterol to CHL1.
Can you also go through my first question please. Thanks

The version mismatch here is irrelevant and you don’t need CGenFF at all. I hope they update the CGenFF server soon so the versions are consistent but you can always check the release notes for what has changed to see if the difference might affect you.

Thanks for your response Dr. Lemkul. Then what I understand is I can take the docked protein-ligand complex directly to gromacs and the pdb2gmx will generate the topology for cholesterol automatically for me. Only thing is that I have to change the name of the ligand to CHL1 in my docked protein-ligand file before giving it to pdb2gmx. Is that correct? Thanks

Yes, and ensure consistency of the atom names.