[gmx-users] H-atoms in .hdb file

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jun 27 08:40:22 CEST 2012

Thanks for your replies.
I found the residuetypes.dat file in top directory of GROMACS package. I need to add the FOR to this file. But it's question for me where am I supposed to set the residuetypes.dat file? In FF folder existed in my working directory?


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, June 26, 2012 8:20 PM
Subject: Re: [gmx-users] H-atoms in .hdb file

On 6/26/12 11:47 AM, Shima Arasteh wrote:
> OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it?

"Dangling bond" errors were introduced as part of the output in Gromacs 4.5. The "aminoacids.dat" file was only used by older (4.0.x and earlier) versions of Gromacs.  You need to be modifying "residuetypes.dat" to indicate that FOR is a Protein residue so that the chain is continuous with respect to its content type.



-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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