[gmx-users] [Fwd: Following your advice to look for the database files...]
David van der Spoel
spoel at xray.bmc.uu.se
Sat Mar 19 13:28:04 CET 2005
> Answering your question I want to mention that we used proDRG to
> receive: 1). PDB file
> 2).GROMACS topology file
> for the I-AEDANS fluorescent probe.
In that case you have to manually merge the topology with the one for your protein. Check
the prodrg tutorial.
> Following your advice to look for the database files I
> found five of them:
> 1. ffg43a1.rtp
> 2. ffg43a2.rtp
> 3. ffg43b1.rtp
> 4. ffgmx.rtp
> 5. ffgmx2.rtp
>When I opened ffg43a1.rtp such a problem occured:
>I can't find any matches between such sort of lines as
>[ bonds ]
>[ angles ]
>[ impropers ]
>[ diherals ]
> in proDRG GROMACS topology file.
>How can I input such lines correctly for my I-AEDANS molecule?
> Thank you for advice
> Senserely yours Vladimir Schepanovsky.
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
More information about the gromacs.org_gmx-users