# Query in devoloping topology regarding **URL:** \ **Category:** User discussions\ **Created:** [January 27, 2025, 7:56am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341 "2025-01-27T07:56:02Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![AISHWARYA01](https://avatars.discourse-cdn.com/v4/letter/a/7993a0/32.png) [@AISHWARYA01](https://gromacs.bioexcel.eu/u/AISHWARYA01)\ **Post date:** [January 27, 2025, 7:56am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/1 "2025-01-27T07:56:02Z")
GROMACS version: GROMACS modification: Yes/No How to generate topology file from pdb. In my case I am using an organic molecule and base to study the simulation. But when I am attempting to generate topology file I am getting error like **residue ligand not found in the residue topology database**. For example i am trying to simulate Naphthalene i am getting error like this.Can anyone explain how to resolve this issue and advice on how to modify my PDB file to ensure compatibility with GROMACS for the topology generation process. ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [January 27, 2025, 11:06am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/2 "2025-01-27T11:06:49Z")
Have you tried converting your pdb into mol2, modifying bond order and then submitting this mol2 structure in the CGenFF web browser? ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 7, 2025, 8:58am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/3 "2025-02-07T08:58:52Z")
No. But i converted pdb to mol2 using swissparam. Still it doesn’t work ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [February 7, 2025, 11:08am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/4 "2025-02-07T11:08:43Z")
Have you edited the header line in the mol2 file? Like, if we open the MOL2 file using any text editor, the molecule header will look like this, “\*\*\*\*”, we have to replace this with our ligand name and make it uniform throughout the MOL2 file. Have you done that? ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 7, 2025, 1:10pm UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/5 "2025-02-07T13:10:20Z")
No what i am conveying is i am not even able to get a mol2 file. With the mol2 file only i can get itp file. But i can’t able to convert pdb to mol2 file. ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [February 7, 2025, 1:39pm UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/6 "2025-02-07T13:39:32Z")
If you have openbabel installed in your system, or any other tools like PyRx, Avogadro, you an easily convert PDB to MOL2. ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 10, 2025, 5:36am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/7 "2025-02-10T05:36:32Z")
Thank you.I did converted it using obabel. But can you tell me from where i can get the itp and other files because i am going to write topol file manually. ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 10, 2025, 5:39am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/8 "2025-02-10T05:39:29Z")
Also you mentioned CGenFF web browser. Is that a liscenced one? ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [February 10, 2025, 6:52am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/9 "2025-02-10T06:52:14Z")
That is a free website. You can register yourself, and generate the ligand topology using the mol2 file you generated. But you need to prepare the mol2 file before submitting it to CGenFF. You can follow this tutorial here ([[link]](http://www.mdtutorials.com/gmx/complex/index.html). ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 14, 2025, 9:35am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/10 "2025-02-14T09:35:57Z")
Thanks i simulated using CGenFF but for some molecule the ligand topology is not generating in CGenFF . I can only able to download str files that shows error like ! “penalty” is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. how should i correct this error. ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 14, 2025, 9:45am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/11 "2025-02-14T09:45:09Z")
readpar debug: read 683 bonds, 2501 angles, 7460 dihedrals, 203 impropers and 375437 characters worth of comments. readmol2 warning: renaming non-unique atom H to H1 . readmol2 warning: renaming non-unique atom H to H2 . Now processing molecule water.pd … paranalogy debug: finding analogy for OGTIP3 HGTIP3 paranalogy debug: finding analogy for HGTIP3 OGTIP3 HGTIP3 paranalogy debug: “smart algorithm” found no matching parameters; switching to “exhaustive algorithm” paranalogy debug: finding analogy for OGTIP3 HGTIP3 paranalogy debug: finding analogy for OGTIP3 HGTIP3 paranalogy debug: finding analogy for HGTIP3 OGTIP3 HGTIP3 paranalogy debug: “smart algorithm” found no matching parameters; switching to “exhaustive algorithm” this is the error file i got ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [February 18, 2025, 12:00pm UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/12 "2025-02-18T12:00:26Z")
That doesn’t seem like an error to me. Check your penalty score. Most likely, if you penalty score is between 10-50 it will still work. If it’s very high like beyond 100, try optimizing your ligand once and generate the topology again. That might helps. ---
**Author:** ![AISHWARYA01](https://avatars.discourse-cdn.com/v4/letter/a/7993a0/32.png) [@AISHWARYA01](https://gromacs.bioexcel.eu/u/AISHWARYA01)\ **Post date:** [February 22, 2025, 3:08pm UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/13 "2025-02-22T15:08:29Z")
I am manually building and optimizing my molecule using Gaussian software. I tried to reoptimize my molecule but still my penalty score is going up to 182. I want to reduce it below 10 so that I will write the topology file using str file. Can you suggest me how should I reduce the score? ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [February 23, 2025, 2:23pm UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/14 "2025-02-23T14:23:21Z")
Citing [CGenFF tools](https://docs.silcsbio.com/2023/cgenff/cgenff.html#practical-considerations): > it should be noted that the CGenFF penalty scores are based on analogy to known parameters. And also very important is that > Accordingly, a parameter with a high penalty may yield acceptable conformational energies, while a parameter already in CGenFF (i.e., penalty = 0) may not yield an acceptable energy surface due to, for example, the terminal rings about the associated bond creating a significantly different context than that in which the dihedral parameter was initially optimized. As such, probably getting better charges with QM methods won’t lower your score, as the comparison will be again done against the same database and it’s not a measure of how good the parameters are in general, but of how similar are they to something already known (and ideally good). So what you can do is i) live with high penalty scores or ii) refine the molecule with the tools I linked or other QM/MM methods. Whatever is your choice, you will then need to benchmark the parametrized molecule to check whether the parameters reproduce the main properties that you need to investigate your scientific problem. ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [February 26, 2025, 6:18am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/15 "2025-02-26T06:18:12Z")
Thank you for your clarification. But it is showing error like this python2 cgenff\_charmm2gmx\_py2.py CLA clath\_fix.mol2 clath\_fix.str charmm36-jul2022.ff NOTE 1: Code tested with python 2.7.12. Your version: 2.7.18 (default, Dec 9 2024, 18:47:23) [GCC 11.4.0] NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: –Version of CGenFF detected in clath\_fix.str : 4.6 –Version of CGenFF detected in charmm36-jul2022.ff/forcefield.doc : 4.6 NOTE 3: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF. what FF do i have to use? The force field i have installed in the latest version i cant able to find any new versions in this? ---
**Author:** ![mnuhu](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@mnuhu](https://gromacs.bioexcel.eu/u/mnuhu)\ **Post date:** [February 26, 2025, 9:15am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/16 "2025-02-26T09:15:19Z")
I am having a problem generating an all-atom topology for a protein with an amino acid residue of 6425 on Charmgui. the error that comes is “Error: float() argument must be a string or a number, not 'NoneType” ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [March 3, 2025, 5:26am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/17 "2025-03-03T05:26:35Z")
It looks like CHARMM-GUI ran into an issue because it’s expecting a number but found something missing instead. This usually happens when there’s a problem with the residue numbering (like having an unusually high number such as 6425), missing atom coordinates a non-standard amino acid or a formatting issue in the PDB file. To fix this you can check if the residue numbering is correct and make sure the PDB file is complete and properly formatted and confirm that the residue exists in the CHARMM force field. ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [March 3, 2025, 6:06am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/18 "2025-03-03T06:06:48Z")
[quote=“MDGRO, post:15, topic:11341, full:true”] Thank you for your clarification. But it is showing error like this python2 cgenff\_charmm2gmx\_py2.py CLA clath\_fix.mol2 clath\_fix.str charmm36-jul2022.ff NOTE 1: Code tested with python 2.7.12. Your version: 2.7.18 (default, Dec 9 2024, 18:47:23) [GCC 11.4.0] NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: –Version of CGenFF detected in clath\_fix.str : 4.6 –Version of CGenFF detected in charmm36-jul2022.ff/forcefield.doc : 4.6 NOTE 3: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF. **what FF do i have to use?** **The force field i have installed in the latest version i cant able to find any new versions in this?** **Any updates in this question?@obZehn@nilanjana88** ---
**Author:** ![MDGRO](https://avatars.discourse-cdn.com/v4/letter/m/a587f6/32.png) [@MDGRO](https://gromacs.bioexcel.eu/u/MDGRO)\ **Post date:** [March 3, 2025, 6:19am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/19 "2025-03-03T06:19:29Z")
[cla.top](https://gromacs.bioexcel.eu/uploads/short-url/xkVSOAjnW9d91RHfU5HDwTZT7uo.top) (7.6 KB) This is my topology file but i am facing the above error in this. Basically what i am trying to do is MD simulation of my molecule which interacts with water at low temperature . For that i am manually editing the topol file(following protein-ligand simulation module in gromacs tutorial). In the place of protein i am taking my manually build optimized molecule and in the place of ligand i am taking water. So basically i am trying to study the interaction between two molecules in the certain temperature. I followed all the steps but in gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr i am facing the above mentioned error. I have attached top file kindly check it. ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [March 18, 2025, 7:06am UTC](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341/20 "2025-03-18T07:06:08Z")
You are referring to water simulation of protein, I suppose. In that case you cannot consider water as ligand. You are studying stability, structure and dynamics of your protein in your preferred water models (TIP3P or SPCE). You need not to generate the water topology separately. There is a tutorial “Lysozyme in water”, read about it and follow the steps. It’s actually easier than a typical protein-ligand simulation. [Next page](https://gromacs.bioexcel.eu/t/query-in-devoloping-topology-regarding/11341.md?page=2)