[gmx-users] fatal error [using pdb2gmx]
Sven Huttenhouse
mdsimulation at hotmail.com
Wed Oct 26 00:15:41 CEST 2005
I'm still not sure that I got the idea. I'm still new to Gromacs
I have a glyc.itp file for a single glycine molecule. It is already included
in the glyc.top file for one glycine molecule. How can I use these files to
get a topology file and a gromacs file (.top & .gro) for 200 molecules??
does this mean that I don't need to use the 200glyc.pdb file for 200
molecules that I have?
kind regards
Sven
>From: David <spoel at xray.bmc.uu.se>
>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: Tue, 25 Oct 2005 21:06:56 +0200
>
>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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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