[AMBER] TI-Amber

From: Ankita Tripathi <at194.snu.edu.in>
Date: Thu, 12 Nov 2020 18:49:31 +0530

Dear Users,
I am very new to thermodynamic integration. I have successfully done the TI
tutorial for amber that is available at
http://ambermd.org/tutorials/advanced/tutorial9 without any problems or

Now I started implementing it on my system which includes one protein and
two ligands Glutamyl phosphate(RGP) and N-Acetyl glutamyl phosphate(UNK),
basically, I wanted to calculate the relative free energy.

I have done the first step in the setup that is Setting up the vdW+bonded
transformation step without any issue after that in the second step Running
MD to provide sane starting coordinates I am getting the following error in
the minimization step
     Mask !:WAT & !.H=; matches 36 atoms
     TI Mask 1 :RGP; matches 22 atoms
     TI Mask 2 :UNK; matches 26 atoms
     TI region 1: 3627 atoms
     TI region 2: 3631 atoms
     SC Mask 1 :RGP.H1,HN1,HN2; matches 3 atoms
     SC Mask 2 :UNK.O5,C6,C7,H6,H7,H8,H9; matches 7 atoms
     Error : Atom 16 does not have match in V1 !

I followed all the key points that are all the common atoms of ligands in
input files have identical starting coordinates, appear in the same order,
share the same atom names.
I am attaching all the required input files.

Any advice, suggestions would be of great help to me!
Thank You in advance.

Kind Regards
Ankita Tripathi

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Received on Thu Nov 12 2020 - 05:30:02 PST
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