Hi,
TLDR: How can I generate GROMACS topology files from a PDB for a small
molecule whose topology is defined in an external OFF library file?
There is a library published by Richard Bryce (
https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off)
for free amino acids compatible with AMBER99SB. What is the cleanest way to
incorporate this OFF library file into my locally installed Amber (24) or
AmberTools (23.6)? Ultimately, I intend to use this library to produce
topology files from PDBs such that they would be compatible with GROMACS,
such as .top and ideally .rtp files. Unsurprisingly, GROMACS pdb2gmx module
can not handle Amber's OFF library files.
Best regards,
D. Yousefi
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Received on Fri May 24 2024 - 03:00:02 PDT
