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

Tue Jul 6 01:47:40 CEST 2010

----- Original Message -----
From: lloyd riggs <lloyd.riggs at gmx.ch>
Date: Monday, July 5, 2010 23:36
Subject: [gmx-users] Re: Re: Fwd: missing atom
To: gmx-users at gromacs.org

> 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. 

Of course it adds hydrogens - that's the purpose of having pdb2gmx use the .hdb hydrogen database. If you actually have evidence of buggy or contradictory behaviour, please file a bugzilla so it can be fixed :-)

> The only problem you may encounter is if you 
> have multiple chains without chain IDs.

That was your problem, but it's not the only one that can happen :-)

> basically, just add -ignh at the end when running a pdb2gmx 
> job.

That means pdb2gmx ignores the hydrogens present in the coordinate file, and generates all from the databases. That may or may not be a good idea in a given case.

>  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.

They're always added back if pdb2gmx finishes without an error. Whether the resulting structure makes sense depends on what you've told pdb2gmx to try to do.

The original poster needs to provide their command line and GROMACS version before they can be given useful help. Before then, they should look at their LEU 2 residue and see what pdb2gmx might be complaining about.

Mark

> 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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