Hi Amber Developers and Users,
My lab and I are trying to simulate a protein unfolding/folding using the SIRAH force field in implicit solvent and were wondering if we could get some help on which implicit solvent model to use.
The Amber user guide mentions that only igb=1 (with DNA) is supported. We did some tests with igb=8 (which we previously used with other all-atom proteins) and we noticed that, at the minimum, the protein did not blow up (though did unfold a little at early stages). I was wondering if the comment in the user guide was due to the fact it was not extensively tested on other implicit solvent models? Or were there other issues that happened during testing? If so, are there any suggestions/recommendations regarding that?
Thanks in advance,
Jeremy Leung
--
Jeremy M. G. Leung
Predoctoral Fellow, Chemistry
Graduate Student Researcher, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml230.pitt.edu<mailto:jml230.pitt.edu> | [He, Him, His]
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 20 2021 - 10:30:02 PDT
