[gmx-users] (no subject)

[Anton Feenstra]

"ôÏËÁÒÅ× áÌÅËÓÅÊ" wrote:
> 
> Hallo!
> I'm simulating a DPPC molecule in water. But
> unfortunatly there is something wrong I don't
> understend.
> Trying grompp with the line
> 
> grompp -f em -p ${MOL}.top -c ${MOL}_w.gro -o
> ${MOL}_gem
> 
> ,I receive wornings like "Invalid directive
> bondedtypes", "Invalid directive ABU", "Invalid order
> in directives atoms" and so on. My .top file contains
> include-string "include ffgmx_.rtp", and in ffgmx_.rtp
> [bondedtypes], [ABU],... are. What's happen? Can you
> help me? Has somebody ever met this problem?

You would probably be missing one of the (obligatory) entries
that must come before [ bondedtypes ]. I don't know right away
what, but it is in the manual, or otherwise have a look at a
generated .top file (e.g. from pdb2gmx). A good rule of thumb
is that all directives must be present, even those that might
appear unnecessary. grompp works rather straightforward in 
that it ignores what it doesn't understand and it doesn't try 
to recover...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Nurture Another Mind, Before Yours Expires" (Arrested    |
|        | Development)                                              |
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