[AMBER] Question on implementing igb=8, along with mbondi3

From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Date: Wed, 3 May 2017 07:26:23 +0000

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


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Received on Wed May 03 2017 - 00:30:03 PDT
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