[gmx-users] about *.itp files

[Anton Feenstra]

David van der Spoel wrote:
> On Fri, 2003-09-12 at 16:00, parinald at unsl.edu.ar wrote:
> 
>>Hi gmx´ers:
>>           I try to create "clna.top". I define a new building block (or 
>>molecule) in the ffG43a1.rtp, then clna.pdb and I don't forget add [CLNA] 
>>in the aminoacid.dat, and now I run pdb2gmx, but dont work`s!.
>>I reed the manual: when defining new molecules (non-protein)it is 
>>preferable to create *.itp (seccion 5.6.2), but I dont know how to use 
>>that!. Thank you. 
>>                 Pablo. 
> 
> we need more information on your molecule.
> is it  a residue in a protein chain or a single molecule? in the latter
> case use the PRODRG webserver.

Since you made an .rtp entry, you already have (nearly) all info you need
to write your own .itp. The main part is changing atom names (as in the .rtp)
to atom numbers (as in the .top/.itp). You may also have to add some parameters.


-- 
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"           |
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