davidlmobley
commented
8 years ago Normally we just modify the topology file to add an [ atomtypes ] section at the top of your topology which defines these atom types (same as the normal atom types, but 0 LJ parameters). However, the tool needs to be modified so it does this itself. Modifying the forcefield .itp files is unnecessary since this info can go into your topology.
For your purposes, you might try adding that section and see if it eliminates this problem. However, ultimately we need to update this tool to do so.
On Sun, Mar 27, 2016 at 3:01 PM, rmuraglia notifications@github.com wrote:
Using the provided example output files from this package, I attempted to run a steepest descent minimization using typical parameters to test my installation. I get the following fatal warning at the grompp step:
" WARNING 1 [file forcefield.itp, line 1]:
Too few gb parameters for type
Couldn't find topology match for atomtype
Abort trap: 6 "
I believe this is because dummy atoms are denoted as "XX_dummy," but this atom type doesn't exist in a standard amber99sb forcefield. In other words, it is not present in my atomtypes.atp, ffbonded,itp nor ffnonbonded.itp files. I'm guessing there are some modifications I must make to these files to make it compatible with the dummy atoms, but it isn't clear to me how I should define them.
An upload of your custom forcefield library seems necessary to complete this distribution.
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rmuraglia
Using the provided example output files from this package, I attempted to run a steepest descent minimization using typical parameters to test my installation. I get the following fatal warning at the grompp step:
" WARNING 1 [file forcefield.itp, line 1]: Too few gb parameters for type
Couldn't find topology match for atomtype **** Abort trap: 6 "
I believe this is because dummy atoms are denoted as "XX_dummy," but this atom type doesn't exist in a standard amber99sb forcefield. In other words, it is not present in my atomtypes.atp, ffbonded,itp nor ffnonbonded.itp files. I'm guessing there are some modifications I must make to these files to make it compatible with the dummy atoms, but it isn't clear to me how I should define them.
An upload of your custom forcefield library seems necessary to complete this distribution.