[gmx-users] Re: Re: Fwd: missing atom

[lloyd riggs]

Dear Abdul Wadood,

So I had the same problem as well.  Basically the pdb2gmx adds all the hydrogens at the end anyways, despite its warnings.  The only problem you may encounter is if you have multiple chains without chain IDs.

basically, just add -ignh at the end when running a pdb2gmx job.  If interactivly, it will ask what you want to do for your ends, N and C terminus, as there are several available types ( NH3, NH2+, Coo-, Cooh, etc...)

It confused me in the beginning as well.  If you look at the out .top and .gro or .pdb you can check if they are added back.

Greetings

Stephan Watkins


Message: 3
Date: Mon, 5 Jul 2010 10:47:12 +0100
From: Oliver Grant <olymacfoogal at gmail.com>
Subject: Re: [gmx-users] Fwd: missing atom
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
    <AANLkTinny_z5lgLBcbtU4voXvpTFc8HphaTs8VBTDvbv at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

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
rest.

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,

Oliver

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
> LEU
>          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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