[gmx-users] fatal error [using pdb2gmx]

Sven Huttenhouse mdsimulation at hotmail.com
Thu Oct 27 21:44:28 CEST 2005


Thank you Dr. David
How do I access the MD randomizer in gromacs?
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
> > >>> > > > 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
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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
> > 
> >>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>++
> > >>>
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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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