[gmx-users] multiple structure .pdb files

David van der Spoel spoel at xray.bmc.uu.se
Sat May 4 11:47:45 CEST 2002

On Fri, 3 May 2002, Attila Borics wrote:

>Hi there!
>I want to analyze a multiple structure pdb-file as a gromacs trajectory,
>but I
>can not convert it to .xtc. I read the FAQ and it said i have to use
>the  -ter option
>to tear the multifile apart to frames. The program said that this option
>does not exist.
>Any ideas what should I do?
You can use the pdb file almost as is, but for gromacs to understand it
you need MODEL and ENDMDL aroun each structure (what they use in NMR

Then you may or may not need a tpr file depending on your analysis

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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