[gmx-users] fatal error [using pdb2gmx]
Sven Huttenhouse
mdsimulation at hotmail.com
Thu Oct 27 19:59:18 CEST 2005
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?
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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>>>--
>>>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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