[gmx-users] error in creat topology

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 23 16:22:32 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
> I want to creat topology file tfe by ffopls.I get pdb file tfe and add
> atoms and bond  tfe atoms to ffoplsrtp file in top file gromacs.so in
> hdd  I add hydrogen atoms.when I do pdb2gmx -f tfe.pdb.I get this
> message:
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
> Residue 56
> Sorting it all out...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.hdb
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa-n.tdb
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa-c.tdb
> Back Off! I just backed up topol.top to ./#topol.top.8#
> Processing chain 1 (9 atoms, 1 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Program pdb2gmx, VERSION 3.3.2
> Source code file: resall.c, line: 436
> Fatal error:
> Residue 'TFE' not found in residue topology database

Then you have done something incorrectly in your creation of the .rtp entry; 
probably incorrect naming.  If you intend on using TFE as a solvent, it is much 
easier to create a simple .itp file for it and #include it in your system 
topology.  Generally, .rtp entries are building blocks for common macromolecules 
(although there are a few exceptions, i.e. NADH, ATP, and a few others commonly 
associated with proteins).


> thank you foe your advise.
> karbalaee
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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