[gmx-users] A problem regarding simulation of SiO2

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 24 21:19:18 CEST 2002

On Wed, 24 Apr 2002, Lianqing Zheng wrote:

>Dear Gromacs team:
>I encountered two problems running Gromacs to simulate Silica(SiO2). First
>one is use pdb2gmx to produce .top or .gro file. The error is:
>Fatal error: Residue 'UNK' not found in residue topology database.
>(I used "UNK" as residue name in the .pdb file.)
>After I changed "UNK" to "SOL", the error became:
>Fatal error: Atom SI in residue HOH 1 not found in database
>             while sorting atoms
Yes, no SiO2 in the database, and it is not water either.

>So I created my own .top and .gro files but got the second problem when
>using grompp command to get .tpr file:
This is fine, but if you want us to look at it, please send the complete
topology and a gro file. It should be quite easy to fix.

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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