Dear all
I'm doing thermodynamic integration to find the free energy of Ca binding
to my protein. The simulations run without issues when I use pmemd. I use a
multisite Ca ion model.
I do 3 steps in protein in water with Ca (restraint addition, charge
removal, and vdW interaction removal). In Ca in water (with no protein) I
do the removal of charge followed by the vdW interaction removal.
Since I want to use QM-MM I wanted to convert my pmemd inputs for sander.
I read the sander tutorial and converted my first step (restraint step) to
sander. (I wanted to first get this step to work before doing the charge
and the vdW steps).
Since sander needs the start and end inputs separately I did that (start
*0* and end *1*).
Previously for pmemd timask1 =90 and timask2 = 91 were used for this step
(two copies of the multisite Ca ion). So for my start and end I thought I
need to have 1 multisite Ca model each in start and end. That makes inpcrd
and promtop files identical (prepared with just the protein and 1 multisite
Ca model) for the start and end.
For pmemd, I restraint the 2nd Ca. Here in sander I only have that
restraint on the end files (*1*) and not on the start files (*0*).
When I ran the restraint step, it fails in the minimization step itself and
the heat step errors with:
""step1_min1.rst" is missing or unreadable"
I have no idea why I get this error? Could somebody please give me
suggestions? Is there an easier way to convert pmemd inputs to sander?
Please let me know if I should provide any additional information.
Thank you so much! I would really appreciate any suggestions or hints.
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Received on Thu Jun 01 2017 - 11:30:03 PDT
