[gmx-users] fatal error [using pdb2gmx]

[Sven Huttenhouse]

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 
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
> >
> >
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> >
>
>
>--
>
>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


>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.

_________________________________________________________________
Don’t just search. Find. Check out the new MSN Search! 
http://search.msn.click-url.com/go/onm00200636ave/direct/01/