[gmx-users] [Fwd: Following your advice to look for the database files...]

[David van der Spoel]

> 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 ]
>gb_2
>gb_20
>gb_26
>gb_4
>gb_9
.......
>[ angles ]
>ga_32
>ga_17
>ga_30
......
>[ impropers ]
>gi_1
gi_1
......
>[ diherals ]
>gd_4
>gd_19
.....    
>   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.
________________________________________________________________________
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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