[gmx-users] fatal error [using pdb2gmx]
David
spoel at xray.bmc.uu.se
Thu Oct 27 20:17:27 CEST 2005
On Thu, 2005-10-27 at 12:59 -0500, Sven Huttenhouse wrote:
> Many Thanks
> I've used the glyc.top file and changed the number of glycin molecules to
> 200 and then used this file as an input for grompp with a pdb file for
> single molecule but it didn't work it gave me this error message:
> number of coordinates in coordinate file (glyc.pdb, 10) does not match
> topology (nglyc.top, 2000).
> I then used my 200glyc.pdb file and it worked fine. I really appreciate your
> help
> But the problem is in my 200glyc.pdb file. I've generated it from a single
> glycine file (glyc.pdb) using genbox with the following command:
> genbox -nmol 200 -ci glyc.pdb -box 3 3 3 -o 200glyc.pdb
> This gave me a box with 200 glycine molecule but most of them are connected
> to each other.
> How can I get a box of 200 glycine molecules that are randomly distributed
> and not attached to each other?
make the original box larger (glyc.pdb). Randomize them using MD.
>
> kind regards
> Sven
>
>
> >From: Oliver Beckstein <oliver at biop.ox.ac.uk>
> >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: Wed, 26 Oct 2005 00:32:36 +0100
> >
> >Hi Sven,
> >
> >>
> >>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??
> >
> >Your topology (topol.top) will look similar to the following
> >
> >--------------------------
> >; this depends on which force field you chose
> >#include ffG45a3.itp
> >
> >#include glyc.itp
> >#include spc.itp
> >
> >; .... perhaps some more stuff
> >
> >[ system ]
> >Box with Glycines
> >
> >[ molecules ]
> >;compound # mols
> >GLYC 200
> >SOL 1234
> >---------------------------------
> >
> >You see, grompp goes through your input configuration (your 200glyc.pdb)
> >and assigns the topologies of the components simply in the order specified
> >in the [ molecules ] sections. Thus, you want to have 200 glycine
> >molecules first, and then (in my example) 1234 solvent SOL (presumably SPC
> >water) molecules. It simply repeats the glyc topology (glyc.itp) 200
> >times. (At least that's my working understanding of the process...)
> >
> >>does this mean that I don't need to use the 200glyc.pdb file for 200
> >>molecules that I have?
> >>
> >
> >You need it as the input for the -c option of grompp. To create your tpr
> >you will have to say something similar to
> >
> > grompp -f my.mdp -c 200glyc.pdb -p topol.top -o run.tpr
> >
> >Hope that helps,
> >Oliver
> >
> >>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
> >>> > > > 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
> >>> >
> >>> >
> >>> > >_______________________________________________
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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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> >>>
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> >>
> >--
> >Oliver Beckstein * oliver at biop.ox.ac.uk
> > http://sansom.biop.ox.ac.uk/oliver/
> >
> >_______________________________________________
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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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