No default angle types, no default proper Dih. types

User discussions
1

GROMACS version:2021.5

I’m trying to do MD simulations of a polymer which I got a topology for in acpype. When I try to run the command

gmx grompp -f ions.mdp -c dpga10_solv.gro -p dpga10n_GMX_OPLS2.top -o ions.tpr

I am getting 350+ errors of the form

ERROR 1 [file dpga10n_GMX_OPLS.itp, line 577]:
  No default Angle types

and

ERROR 20 [file dpga10n_GMX_OPLS.itp, line 814]:
  No default Proper Dih. types

Checking my itp file, I found that several lines where there should be an OH had just ‘x’, e.g.:

image
image849×185 4.86 KB

so I went through the itp file and manually changed these lines to have OH, but the lines which had x’s are still giving the errors shown above. Any help is appreciated, happy to provide any other information.

2

Everything after the ; are comments and ignored by GROMACS. What I think ACPYPE is telling you in the comment is that the lines with x in the interaction atom types (the last three values in the comment) could not be found in the force field. You will have to generate parameters for these interactions yourself, or possibly set them based on very similar interactions. Keep in mind that it is important that you check that your parameters are correct, regardless of how you generate/assign them.

What force field are you using? It is also possible that another force field contains parameters for these bonded interactions. So, if you can switch force field, it might be worth trying that.

3

ACPYPE OPLS was “very” experimental and I strongly advise to not use it unless you really know what you’re doing. And yes, ‘x’ is an unknown atom type.

See: https://github.com/alanwilter/acpype/blob/1386573fc3a3f655ff8c6c21313454c61c4450b9/NOTE.txt#L36 (but I can’t help, consider MKTOP).

You may also check this https://code.google.com/archive/p/acpype/wikis/TutorialAcpype4GromacsOPLS.wiki but it’s quite old and outdated.

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