[gmx-users] Topology File

[Anton Feenstra]

Albert Sun wrote:
> Dear Users,
> 
> I wrote my own  .top  file and  ran the  em.mdp, here are errors 
> 
> WARNING 1 [file "try1.top", line 18]:
>   Invalid directive atom
> WARNING 2 [file "try1.top", line 22]:
>   Too few parameters on line (source file toppush.c, line 673)
> WARNING 3 [file "try1.top", line 23]:
> 
> 
> could you advise me how to avoid the errors?  I  attached my .top here.

I'm sorry, but you will have to do that all by yourself. It's a lot of
work, I know from experience, but you will simply have to work through it.
Read the topology chapter in the manual. Look at a couple of existing
topology files (e.g. from pdb2gmx, ProDrg, directory $GMXDATA/share/top)
to see how it is  done. Read the error messages carefully.

If that still leaves you stuck, feel free to ask again on the list.
It would help to know what molecule you are working on...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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