Dear Gunnar, I am right now on holidays but in 2 weeks I can help you with antechamber unix problems you may be facing.
For the moment I suggest you to read acpypi and antechamber documentation with attention, practice the tutorials and examples. I understand that many users urge to use such tools straightaway, but believe me, although antechamber and acpypi can save you a lot of time and effort, this will only pay off if you do your homework properly. Thanks to Mark and Justin for addressing his questions. Cheers, Alan On Sun, Oct 25, 2009 at 20:30, <[email protected]> wrote: > Gunnar Widtfeldt Reginsson wrote: >> Hi. >> I need to create a topology file for a small organic molecule that is to >> interact non- covalently with a DNA duplex. I want to use the amber99 >> force field. >> I saw on this mailing list that you can use acpypi with antichamber to >> create a topology for amber force fields. I got the amber10 tools and >> installed but I couldn't find any more information on how to get the >> antichamber package to work. I am finding this all very complicated >> since I am not an expert in the unix language, so if anyone knows about >> a good beginners tutorial on how to install antichamber and acpypi could >> you please let me know were to find it. > > http://www.google.com.au/search?q=+antechamber+tutorial > > Note spelling of "antechamber". > >> Another question is, how difficult is it to create the topology for the >> molecule by hand for the amber99 force field. Could someone please get >> me started on that, if it would be easier. The molecule is a derivative >> of cytosine. > > Non-experts should use antechamber (and most experts too!) > > Mark > >> I am using GROMACS 4 on Mac OS 10.5 >> >> Thanks. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
