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

[Shima Arasteh]

As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose none as the N-terminus . But after processing the .pdb file the FOR is identified itself but "not" identified as protein. 

Any suggestion please?

Thanks in advance
Sincerely,
Shima


________________________________
From: Mark Abraham <mark.abraham at anu.edu.au>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
Sent: Wednesday, June 27, 2012 11:54 AM
Subject: Re: [gmx-users] H-atoms in .hdb file


On 27/06/12, Shima Arasteh  <shima_arasteh2001 at yahoo.com> wrote:
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?

Apparently it's not been done right, but we don't have enough detail about what you've done to know what you've done wrong. Look carefully at the contents of the file you changed, and inspect your output carefully for clues.

Mark

>
>Thanks in advance
>
> 
>Sincerely,
>Shima
>
>
>----- Original Message -----
>From: Justin A. Lemkul <jalemkul at vt.edu>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Cc: 
>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.
>
>http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
>-Justin
>
>-- ========================================
>
>Justin A. Lemkul, Ph.D.
>Research Scientist
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
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