[gmx-users] fatal error [using pdb2gmx]
David
spoel at xray.bmc.uu.se
Thu Oct 27 22:27:22 CEST 2005
On Thu, 2005-10-27 at 14:44 -0500, Sven Huttenhouse wrote:
> Thank you Dr. David
> How do I access the MD randomizer in gromacs?
Just put your glycines in a box with water and run MD.
Dye to different starting velocities they will randomize very quickly.
> 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: Thu, 27 Oct 2005 20:17:27 +0200
> >
> >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
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> > > >>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > >>> > > > Please don't post (un)subscribe requests to the list. Use the
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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
> > > >>> >
> > > >>> >
> > > >>> > >_______________________________________________
> > > >>> > >gmx-users mailing list
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> > > >>> >
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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
> > >
> > >>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >++
> > > >>>
> > > >>>_______________________________________________
> > > >>>gmx-users mailing list
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> > > >>
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> > > >>_______________________________________________
> > > >>gmx-users mailing list
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> > > >>
> > > >--
> > > >Oliver Beckstein * oliver at biop.ox.ac.uk
> > > > http://sansom.biop.ox.ac.uk/oliver/
> > > >
> > > >_______________________________________________
> > > >gmx-users mailing list
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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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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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