Re: [AMBER] Termodinamic Integration setup error

From: Hannes Loeffler <>
Date: Thu, 17 Dec 2015 09:59:01 +0000

On Thu, 17 Dec 2015 10:46:17 +0100
Claire Coderch Boué <> wrote:

> Dear AMBER users,
> I am trying to get familiar with the TI protocol as seen in the online
> tutorial:
> 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.

But do the coordinates match? The code checks for this and allows
deviations of up to 0.1 Angstrom per direction (x, y, z). That error
message is not very informative in this respect.

Also, why do you use a dual-topology approach (softcore) for only two
atoms (and disconnected ones)? You could just transform all your atoms
linearly into the final type.


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Received on Thu Dec 17 2015 - 02:00:04 PST
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