Including parameters in an itp file in topology

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1

GROMACS version: 2021
GROMACS modification: No
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Hi GROMACS: I have parameters from the literature packaged in an itp file. I added the atomtypes from there into the appropriate rtp files and I am able to build a topology, but this topology does not contain the parameters from the itp file. I tried #include {itp file} in forcefield.itp but that had no effect. How can I ensure that ALL the bond, angle, and dihedral parameters in my itp file will be incorporated into the topology generated by pdb2gmx? There seems to be no option for including additional itp files…

Thank you very much!
Dan

2

Hi,
If you have included the bond terms in the bonded.itp file (forcefield files), and the molecule topology is properly defined. You might not see the parameter values in the topol.top file, since they may be directly taken from forcefield files. Did you check for it?

Or Is itp file already describing a molecules (it contains the directive [moleculetype]) ? Than an alternative is to directly include the file in topol.top (taking care to avoid duplication of [moleculetype] definition).

I hope it helps
Alessandra

\Alessandra

3

I included the bond terms in the itp file but the topol.top doesn’t include them. If I remove the itp file completely, the topology still builds “normally”. It clearly isn’t including the itp file. How can I make sure it is included? I edited the atomtypes and aminoacids.rtp file and that information is being included but not the bond/angle/dihedral terms from the itp. The itp does not have a [molecule type] directive.

4

Hi,
Topologies are built in hierarchical way. The following table provides the order in which the information has to be provided in topology files File formats — GROMACS 2022.1 documentation
maybe it can helpful.

Sorry I did not understand where you have included the itp and which format has your itp. In general, the bond parameters are defined in bonded.itp. This file is included in forcefield.itp.

If the interactions (not parameter) are defined in the topol.top generated by gmx pdb2gmx then you can try to run one step to check that the bond parameters are read properly from the bonded.itp file

\Alessandra