[gmx-users] Re: Creating topology for a small organic molecule

Alan alanwilter at gmail.com
Mon Oct 26 19:10:03 CET 2009

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.



On Sun, Oct 25, 2009 at 20:30,  <gmx-users-request at gromacs.org> 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)

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