Dear Amber Users,
I am trying to simulate the chloride transport by some organic molecules
across a POPC membrane, with explicit TIP3P solvation, using steered MD and
afterwards umbrella sampling on evenly spaced snapshots to perform PMF
calculations. This is the same methodology used in several papers on anion
carriers (eg. DOI: 10.1039/c8cp02576b or 10.1039/d1ob01279g). Performing
the SMD simulations and US with just chloride or the organic molecules alone
worked just fine, but when I tried to simulate the complex with chloride I
found that the anion leaves the complex quite fast (first picoseconds of the
simulations). To avoid this I have tried to put restraints on the distances
between the chloride and some atoms of the organic molecule and this keeps
the anion in place during normal simulation (not SMD), but if I try to
include these restraints during the pulling phase of an SMD run, I get the
following error:
jar option running
In Jarzynsky runs, there must only one restrain, stopping program
Is there any way around this?
Besides, I wonder if having restraints between the chloride and the organic
molecule during the US calculations, where I already need to have restraints
to keep the complex in a certain location relative to the center of the
membrane, would be appropriate for the purpose of calculating the PMF
profiles.
Any comments on these would be very much appreciated.
Jordi
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Jordi Bujons, PhD
Dept. of Biological Chemistry (QB)
Institute of Advanced Chemistry of Catalonia (IQAC)
National Research Council of Spain (CSIC)
Address: Jordi Girona 18-26, 08034 Barcelona, Spain
Phone: +34 934006100 ext. 437684
(direct) +34 934006143
FAX: <tel:%2B34%20932045904> +34 932045904
<mailto:jordi.bujons.iqac.csic.es> jordi.bujons.iqac.csic.es
<
http://www.iqac.csic.es/>
http://www.iqac.csic.es
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Received on Wed Mar 01 2023 - 03:30:02 PST
