Dear Amber users,
I would like to simulate interactions in systems composed of antibiotics
and polymers that are built using the GAFF2 force field with lipid bilayers
and DNA. On the Amber website (
https://ambermd.org/AmberModels.php) for
simulating bilayers and DNA, two force fields are recommended: LIPID21 and
BSC1,
My questions are as follows:
1. Is GAFF2 more appropriate than GAFF force simulation, in a case when
polymers and antibiotics are combined specifically for lipids and DNA force
fields? I found similar studies in which the GAFF force field was used for
ligands and polymers. It is possible that GAFF2 is a new force field that
does not interact with the force fields LIPIDS21 and BSC1.
2. What method of calculating partial charges for polymers and antibiotics
is more appropriate for HF/6-31G* (RESP) or the new AM1-BCC for GAFF2, that
is, ABCG2, when
(i) Simulated interactions between polymers and antibiotics in a water box
(ii) When do polymers and antibiotics in GAFF2 interact with the lipid
bilayers or DNA in LIPIDS21 and BSC1 in the water box, respectively?
Best regards,
Victor
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Received on Fri Jan 17 2025 - 03:00:03 PST
