Re: [AMBER] stfcdiffusion error

From: Daniel Roe <>
Date: Wed, 22 Jan 2014 14:32:36 -0700

Hi, sorry for the delay in replying.

This message means that there were no atoms in mask between 1.0 and 6.0
Angstroms away from atoms in mask2. I think the likely cause is that your
atom mask for mask2 (:.O4*) is invalid; you should have received an error
message like "Error: empty token for ':'". Remove the residue ':' character
so you have:


Hope this helps,


On Wed, Jan 15, 2014 at 7:43 PM, Diego de paula <>wrote:

> Dear all,
> I have simulated a surface that interacts with ions using the PMEMD code on
> AMBER12. I try to run the stfcdiffusion command with the proper flags
> (stfcdiffusion mask .I- mask2 :.O4* lower 1.0 upper 6.0 out diffusion.dat
> com) but I found the error "No atoms of mask 1 left for processing". I have
> used the unwrap command to correct the wrapped system. I think that the
> analysis fall down when no atom are found in the layer. Could someone
> explain me what is wrong?
> --
> Diego de Paula Santos
> Doutorando em Química
> Universidade Federal de Pernambuco
> Centro de Ciências Exatas e da Natureza
> Departamento de Química Fundamental
> Laboratório de Química Téorica e Computacional
> Contato: 2126-8440 ramal 5007
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 22 2014 - 14:00:02 PST
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