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

[Christopher Neale]

Excellent blind diagnosis Mark!

VMD molefacture seems to build leucines with nearly linear CA-CB-CG angles. In one case I got an angle that was exactly linear, hence the problem for pdb2gmx to build the hydrogens. I'll report to VMD; I'll also file an enhancement request for pdb2gmx to provide an error or warning when hydrogen atom coordinates are set as -nan.

Thank you,
Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: 18 April 2014 01:32
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms

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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