How to solve the " No default Proper Dih. types" in GROMACS-5.1.4 using CHARMM36feb2021.ff?

Command line:
gmx grompp -f minim.mdp -c 1yamb_ego_sol.gro -p topol.top -o em.tpr

NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 422228852
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations

ERROR 1 [file ego.itp, line 76]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘EGO’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Cleaning up constraints and constant bonded interactions with virtual sites
Removing all charge groups because cutoff-scheme=Verlet

There was 1 note


Program gmx grompp, VERSION 5.1.4
Source code file: /home/npp/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 1738

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Dear Anonymous Colleague,

First of all, more courtesy would help here. E.g. address your readers, state your problem, make it understandable to your peers, think about reproducibility, sign it under your name etc. Also please familiarize yourself with the layout of the forum and post your request in the appropriate section (Site feedback is for reporting bugs/questions about the forum itself).

We are a community of unpaid volunteers and GROMACS users, helping out each other. Just posting the output of a script is rude, don’t do this if you expect a helpful reply.

Kind regards,

Andras

Dear Awacha,
I am Subhasree Ghosh, pursuing my PhD in the field of Biotechnology and Bioinformatics in the University of Hyderabad.
I am extremely sorry for the inappropriate approach of conveying the problem. I am new in this and today I opened my account. Thank you so much for your suggestions and guidance and I will try to follow the same. I apologise once again.
Actually I am using gromacs 5.1.4 and Charmm36 feb2021. I have generated the itp files for ethylene glycol and other diols in CGenFF (version 4.5). But the charmm36 feb2021 is of version 4.4. and the latest version of charmm36 jul2021 is of version which is not compatible with gromacs 5.1.4.now when I am using this itp files in the step before
energy minimization step it’s showing this error l stated in the previous comment. And I have to use tip4p2005 water model for that also I need itp and gro file. Itp file I got it from GitHub but where I can get the gro file for tip4p2005 water model that also I want to know. Please help me with this and guide me how I can improve my understanding in this field.

Thanks and regards,
Subharee

1 Like

Please move this discussion in its entirely (full context) to the User Forum. This is the wrong venue for this discussion.

1 Like

Dear @jalemkul, could you please move the discussion? Just being promoted to trust level 2 (“member”), I don’t have the privileges to do this. Thank you!

I have no administrator rights to do stuff like that. OP needs to make a new post in the right forum.

Dear Subharee,
sorry for my rude words, it was out of line.
Your second post clarifies many things. As you have guessed, the error you get is indeed the consequence of the mismatch in the CGenFF version. Since to my best knowledge, you cannot select an earlier version in the CGenFF server, you might need to update your GROMACS version. Generally, if you do not have a strong reason against it, you should definitely use a more recent version: many bugs were fixed, and efficiency was strongly improved since 2016.
Note that this kind of error (missing parameters) are reported by the grompp subprogram: pdb2gmx does not check the validity and completeness of the topology it creates.
I have found files for the tip4p2005 model here: GROMACS files for the TIP4P/2005 model page on SklogWiki - a wiki for statistical mechanics and thermodynamics (I take no responsibility for it, however ;-)). They also give the coordinates of a box of 360 water molecules in a .g96 file, which GROMACS accepts almost everywhere in place of a .gro file (see the on-line help of the gmx subcommands).
Please note however that many force fields were parametrized with a specific water model in mind: in the case of CHARMM, this is a version of TIP3P. Using a different water model might be permissible, but you need to have solid arguments for that. You might run into other problems, too. In this case e.g. the electrostatic and VdW cut-offs in CHARMM are 1.2 nm (Force fields in GROMACS — GROMACS 2022 documentation), while the above mentioned site for the tip4p2005 model recommends a 0.85 nm cut-off.
This field is a vast one. You can find very good introductory material in the GROMACS manual itself, @jalemkul’s tutorials, and in the “Best practices” papers in the “Living Journal of Computational Molecular Science” (http://livecomsjournal.org).
I hope that helps.
Kind regards,
Andras

Dear Awacha,
Thank you so much for the clarification and I really appreciate your efforts you did to clear my doubts. I will try and will keep in touch for further information. As I am new in this field it is going to be very helpful for me.

Thanks and regards,
Subhasree