[gmx-users] Fwd: missing atom

Oliver Grant olymacfoogal at gmail.com
Mon Jul 5 11:47:12 CEST 2010

Dear Abdul,

I had a similar error always with residue number 2 when using the amber
ports in gromacs. Manually adding the hydrogen to the backbone nitrogen that
connects to residue 1 will fix this.

You might know how to do this but just in case here is how I do it:

load your pdb into any builder and add the hydrogen into a reasonable
position(i.e no steric clash) on the nitrogen. write out a pdb. I find that
builders can change the format of pdb's so I usually just copy the H line
and add it into my original pdb formatting it as needed.

It is the only H that needs to be defined. pdb2gmx will take care of the

I'm not sure why this happens but I didn't look too much into it at the time
as I was learning how to use gromacs and everything was going wrong :)

Hope this helps,


On 3 July 2010 16:50, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> Dear Abdul,
> please keep all Gromacs-related questions on the mailing list.
> Best,
>   Carsten
> Begin forwarded message:
> *From: *"abdul wadood" <wadoodbiochemist at hotmail.com>
> *Date: *July 3, 2010 8:40:29 AM GMT+02:00
> *To: *<ckutzne at gwdg.de>
> *Subject: **missing atom*
> Dear Carsten
> I am running simulation using gromacs with amber forcefields on my protein.
> I have prepared the input file accordingly and have all the required
> library. But the problem is that when i run pdb2gmx for the top file the
> following error come:
> WARNING: atom H is missing in residue LEU 2 in the pdb file
>          You might need to add atom H to the hydrogen database of residue
>          in the file ff???.hdb
> I tried my best to solve the problem, searching on the gromacs website and
> manual but cannot succeed.
> If you kindly help me in this respect your help will be highly appreciated
> by our group our research.
> the input file is attached.
> Many regards
> Abdul Wadood,
> Research Scholar,
> Dr.Panjwani Center for Molecular Medicine and
> Drug Research,
> International Center for Chemical and
> Biological Science,
> University of Karachi, Karachi-75720, Pakistan.
> Email:wadoodbiochemist at hotmail.com
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