[gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms

[Mark Abraham]

Well, it is building hydrogen atoms, and that could go astray if the
coordinates from which they are built are badly behaved (e.g. co-linear).

Mark


On Fri, Apr 18, 2014 at 4:47 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> In most cases, I get what I expect when I execute the following command:
>
> echo -e "6\n1\n" | pdb2gmx -f ${b}e.gro -o ${b}et.gro -p tmp.top -i
> ${b}_posre.itp -ter -ignh
>
> However, I have one input .gro file for which the output .gro file has
> -nan for all coordinates for HB1 and HB2 atoms. I built the input .gro file
> using molefacture in VMD, and maybe it is not perfect, but I was under the
> impression that pdb2gmx didn't care about coordinates, so I am stumped
> about what could be the problem.
>
> Got same result with 4.6.1 and 4.6.5. Also a second run through pdbtgmx
> (giving the output .gro from first round as input .gro to second round)
> gave the same results.
>
> Has anybody else run into this? If not, I'll file a redmine.
>
> Thank you,
> Chris.
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