[gmx-users] fatal error [using pdb2gmx]

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 24 20:45:19 CEST 2005

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).



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
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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
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