[AMBER] Termodinamic Integration setup error

From: Claire Coderch Boué <anyron.gmail.com>
Date: Thu, 17 Dec 2015 10:46:17 +0100

Dear AMBER users,

I am trying to get familiar with the TI protocol as seen in the online
tutorial: http://ambermd.org/tutorials/advanced/tutorial9/#home

I have already run it without any problems or warnings in one of my
systems. But now I'm getting the following error in the minimization phase:

     Mask !:WAT & !.H=; matches 34 atoms
     TI Mask 1 :SS2; matches 25 atoms
     TI Mask 2 :SS1; matches 25 atoms
     TI region 1: 3736 atoms
     TI region 2: 3736 atoms
     SC Mask 1 :SS2.H6,H7; matches 2 atoms
     SC Mask 2 :SS1.Cl1,Cl2; matches 2 atoms
     Error : Atom 9 does not have match in V1 !

I cannot find any explanation of this error online.

My system has been extracted directly from the PDB and the changes that are
studied are the change from H to Cl, which does not alter the initial
conformation of the ligand. So the two systems that are being studied are
and exact replica of each other except for the two Cl atoms. Preps
coincide, pdb coincide, so I have no idea of what is happening.

Can anyone explain to me what this error means so I might find what is

Thank you very much,

Faculty of Pharmacy
Universidad CEU San Pablo
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Received on Thu Dec 17 2015 - 02:00:03 PST
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