[gmx-users] Trouble creating topology file

[David van der Spoel]

On Tue, 8 Feb 2005, Bill Evans wrote:

>Hi,
>
>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.
________________________________________________________________________
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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