Dear Amber experts,
I am using Amber/20 and submodule antechamber for nonstandard residue force field preparation. My nonstandard residue is a covalently modified residue and it is part of the protein structure. I would greatly appreciate it if anyone could help with some difficulties I met when using parmchk2.
To prepare the force field parameters, the common steps I take are as follows:
1 Use antechamber to assign partial charges and the amber atom types to the atoms.
2 Use prepgen to generate the prep input files.
3 Use parmchk2 to generate parameters, according to the atom types in the .ac file, which was initially generated in step 1, and was modified in step to get rid of the capping atoms of the residue.
In this step, we will run parmchk2 twice, and let the source dictionary of parameters be gaff2 and parm10 (ff14SB), respectively.
4 When using the resulted parameter modifications files, we will load the gaff2.frcmod first, then load the parm10.frcmod to overwrite as many parameters as possible. We were under the impression that this is a way to parameterize the residue in a combined ff14SB-gaff2 manner, and ff14SB will be the dominant source of parameters.
Today I was dealing with a residue including one atom that could not be assigned to any amber atom types. If any atom gets the atom type DU in the .ac file, parmchk2 will not be able to process it.
I figured that a walkaround would be, to use the gaff2 atom types from beginning. However, if the atom types are gaff2, I couldn’t get any parm10 parameters out of it. (On the contrary, if the atom types are amber, parmchk2 is able to match the amber atom types with gaff2 atom types. This is likely because gaff2 atom types are more generic and there is always one reliable solution to map amber to gaff2, but not for aagaff2 to amber)
It is possible to manually modify or to concatenate the parameters in some way, to get the frcmod file I want. Still I wish parmchk2 were able to process the rest of the residue, and mark the missing parameters due to presence of DU…
Has anyone dealt with similar situations before? Any comments/suggestions would be greatly appreciated 😊
Many Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
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Received on Sat Aug 27 2022 - 20:00:02 PDT
