[gmx-users] fatal error [using pdb2gmx]

Tue Oct 25 21:06:56 CEST 2005

On Tue, 2005-10-25 at 14:01 -0500, Sven Huttenhouse wrote:
> Thans alot for your help.
> I've generated the 200glyc.pdb file using genbox (which enable you to 
> riplicate the molecule you have) and viewed the 200glyc.pdb file using vmd 
> and it showed separate (full glycine) molecules
> I then used pdb2gmx to generate the .gro file, I used the following command:
> pdb2gmx -ignh -f 200glyc.pdb -p 200glyc.top -i 200glyc.itp -n 200glyc.ndx -o 
> 200glyc.gro.
> I then choosed force field # 3 and I got all the files. However when I 
> viewed the 200glyc.gro file with vmd I found separate molecules but they are 
> not full glycine, they have one missed Oxygene atom and two missed Hydrogen 
> which are supposed to be connected to the Nitrogene. The first Glycine 
> molecule was full molecule but the successive molecules were not. I got this 
As someone said previously: pdb2gmx connects all the residues. Read
previous mails about your question.


> from the 200glyc.gro file I have:
> 
> GLYCINE GEOMETRY
> 1403
>     1GLY      N    1   1.255   0.309   0.930
>     1GLY     H1    2   1.326   0.326   0.998
>     1GLY     H2    3   1.206   0.224   0.952
>     1GLY     H3    4   1.297   0.300   0.840
>     1GLY     CA    5   1.159   0.421   0.929
>     1GLY    HA1    6   1.118   0.429   1.020
>     1GLY    HA2    7   1.209   0.505   0.907
>     1GLY      C    8   1.052   0.398   0.826
>     1GLY      O    9   1.059   0.283   0.754
>     2GLY      N   10   2.840   0.560   1.456
>     2GLY      H   11   2.940   0.565   1.459
>     2GLY     CA   12   2.698   0.558   1.494
>     2GLY    HA1   13   2.645   0.605   1.424
>     2GLY    HA2   14   2.668   0.463   1.501
>     2GLY      C   15   2.679   0.627   1.627
>     2GLY      O   16   2.790   0.678   1.686
>     3GLY      N   17   2.757   1.988   2.346
>     3GLY      H   18   2.739   2.086   2.333
>     3GLY     CA   19   2.806   1.890   2.445
>     3GLY    HA1   20   2.792   1.798   2.408
>     3GLY    HA2   21   2.903   1.905   2.460
>     3GLY      C   22   2.730   1.904   2.574
>     3GLY      O   23   2.635   2.000   2.5
> 
> So what do you think the problem is??
> 
> kind regards
> Sven
> 
> >From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] fatal error [using pdb2gmx]
> >Date: Mon, 24 Oct 2005 19:45:19 +0100
> >
> >Hi Sven,
> >
> >Besides, you're better off with a topology (.itp) for a single glycine 
> >which
> >you #include in the .top file, rather than running the box with 200 
> >glycines
> >through pdb2gmx. The program would fail to notice that the molecules are 
> >not
> >attached to each other, unless you give them all unique chain identifiers 
> >:p
> >or have a TER statement after every single glycine. But in that case 
> >pdb2gmx
> >will generate 200 .itp files for you, which may also not reflect your 
> >needs.
> >Check the topology file section in the manual (chapter 5).
> >
> >Cheers,
> >
> >Tsjerk
> >
> >On 10/24/05, Erik Lindahl <lindahl at sbc.su.se> wrote:
> > >
> > > Hi,
> > >
> > > Fatal error: Atom H1 in risidue GLY 2 not found in rtp entry with 7 
> >atoms
> > > while sorting atoms. maybe different protonation state. remove this 
> >hydrogen
> > > or choose a different protonation state. Option -ignh will ignore all
> > > hydrogens in the input.
> > >
> > > I used force field # 3. Could you please explain to me how can I solve
> > > this?
> > >
> > >
> > > GROMOS96 45a3 is a united-atom force field, i.e. nonpolar hydrogens are
> > > merged with the carbons. Use the option "-ignh" to ignore the hydrogens 
> >in
> > > the input coordinate file, or choose an all-atom force field like 
> >OPLS-AA/L
> > > instead.
> > >
> > > Cheers,
> > >
> > > Erik
> > >
> > > -----------------------------------------------------------
> > > Erik Lindahl <lindahl at sbc.su.se>
> > > Assistant Professor, Stockholm Bioinformatics Center
> > > Stockholm University, SE 106 91 Stockholm
> > > Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
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> > >
> > >
> >
> >
> >--
> >
> >Tsjerk A. Wassenaar, M.Sc.
> >Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> >Dept. of Biophysical Chemistry
> >University of Groningen
> >Nijenborgh 4
> >9747AG Groningen, The Netherlands
> >+31 50 363 4336
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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