[gmx-users] Re: Problems with the file 2J3Q.pdb and residue 'TFL'

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 20 18:49:00 CET 2007

Captain_Gray wrote:
> Dear sirs,
> I'am trying to use the file 2J3Q.pdb (downloaded from your protein bank)
> with the program Gromacs 3.3.2, and I have great problem,
> after inputting a command:
> pdb2gmx -f 2J3Q.pdb -water spc -ignh
> I receive a fatal error: Residue 'TFL' not found in residue topology 
> database.
> Would you be so kind to explain what I should do in order to miss this 
> error?
> All that I want is to take out a structure of Thioflavin T from some 
> other big sctructure, and do some
> operations with it in Gromacs.
> p.s. I am russian student, and just trying to write some term paper 
> about Gromacs and ThT.
Try reading on the wiki.gromacs.org
The residue is not a standard amino acid therefore it is not supported 
straight of.

Please ask further questions on the mailing list.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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