[gmx-users] fatal error [using pdb2gmx]
Oliver Beckstein
oliver at biop.ox.ac.uk
Wed Oct 26 01:32:36 CEST 2005
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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--
Oliver Beckstein * oliver at biop.ox.ac.uk
http://sansom.biop.ox.ac.uk/oliver/
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