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

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jun 27 09:10:35 CEST 2012

I added the FOR residue as protein in residuetypes.dat file, but still says it's not identified as protein/DNA/RNA. 

Would you mind helping me with your suggestions?

Thanks in advance


----- 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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