[gmx-users] Trouble creating topology file

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 8 23:32:02 CET 2005

On Tue, 8 Feb 2005, Bill Evans wrote:

>I am trying to create the necessary .top file using pfb2gmx. I start 
>with what seems to be a valid  .gro file. It consists of a box that is 
>1/2 SI and O and 1/2  flexspc water. I get the output shown in the 
>attached file. I checked the database files and SI and O seem to be 
>valid atom types. The bottom line is that an error is given:  "Fatal 
>error: Residue ' ' not found in residue topology database"
Yes, you need to get the topology in a different manner, because glass is 
not a protein. Try without water first, using x2top. Search the mailing 
list for x2top to get more hints.

>Can someone point me in the right direction to resolve this error?

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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