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

[Justin A. Lemkul]

On 6/27/12 6:38 AM, Shima Arasteh wrote:
>
>
> I added this line to the residuetypes.dat file:
> FOR   Protein
>
> Then running this command:
> pdb2gmx -f protein.pdb -water spc -ter
>
> Written as blow:
>
> Processing chain 1 (177 atoms, 25 residues)
> Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
> Identified residue VAL1 as a starting terminus.
> Identified residue GLY24 as a ending terminus.
>
> Asked for terminus:
> I chose "none" as the N-terminus.
>
> Getting this:
>   Processing chain 1 (177 atoms, 25 residues)
> Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
> Identified residue VAL1 as a starting terminus.
> Identified residue GLY24 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for VAL-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus VAL-1: None
> Select end terminus type for GLY-24
>   0: COO-
>   1: COOH
>   2: None
> 0
> End terminus GLY-24: COO-
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.5
> Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
>
>
> Would you helping me with it with your useful suggestions?
>

I honestly have no idea why that's not working.  It's the exact same workflow 
used with all other capping groups and I use it routinely.

-Justin

-- 
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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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