[gmx-users] Residue 'SIA' not found in residue topology database

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 8 09:19:14 CEST 2007


A force field is not a magic thing (nor is an MD package). It can only
deal with molecules or building blocks which are in the database or
provided otherwise. Something like this requirew parameterization.
You're not up to that at this point (said with didactical intentions).
Learn to walk before you try running (right Mark?). First get yourself
going with a standard system, and get the hang of simulations,
including a thorough read of background theory: possibilities and
limitations, force fields, parameterization, etc.


On 5/8/07, kong.winter <kong.winter at gmail.com> wrote:
> Hi all,
> when I use the following command:"pdb2gmx -f 1G1T.pdb -p gr.top -o gr.gro"
> There's a fatal error:
> Residue 'SIA' not found in residue topology database
> I checked the PDB file, the following details:
> HET           SIA  C 601      20
> FORMUL     2  SIA    C11 H19 N1 O9
> ..........
> Who knows how to solve it?
> Any tip is appreciated, thank you very much.
> Best,
> Winter
>  ________________________________
> kong.winter
> 2007-05-08
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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