Dear All
If I have a solvated trajectory at the end of my simulation, and now would want to run implicit solvation GB/SA model based on that trajectory previously obtained from explicit solvent, how do I get that done?
In fact, I wrote the following script in cpptraj and the pdb file it gave me had 8000 models corresponding to the 8000 frames of my solvated trajectory.
I am confused here. My plan was to create a pdb from that solvated trajectory. Then using tleap, and switching to mbondi3, get my starting parameter and coordinate files to run GB/SA method with igb=8.
Can you please give me some insight on what I did/am doing wrong? Is there any other way I should be pursuing to implement implicit solvation method based on a solvated trajectory?
parm revnelson.smd.prmtop
trajin smd.mdcrd
strip :WAT
center :1-24 mass origin
image origin center familiar
trajout smdgb.pdb pdb nobox
My deep apologies if this looks simple
Regards
Ramin
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Received on Wed May 03 2017 - 00:30:03 PDT
