[gmx-users] about *.itp files
feenstra at chem.vu.nl
Mon Sep 15 09:37:04 CEST 2003
David van der Spoel wrote:
> On Fri, 2003-09-12 at 16:00, parinald at unsl.edu.ar wrote:
>> 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.
> 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.
| | |
| _ _ ___,| 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/ |
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