Nicolas Lux Fawzi wrote:
> Hi Professor Case,
> Thanks for your response.
> Yes, I really do have a 3 component system : multiple peptides (on the
> order of 20), multiple organic solvent molecules (glycerol, which i
> created in antechamber with gaff), and multiple waters.
> I suppose I could make a pdb file with the correct ratio of glycerols to
> peptides, replicate that manually/periodically enough times to get the
> system size I want, then solvateBox to add the water. I was wondering
> if there was an easier way that didn't involve manual placing of all the
> peptides and organic molecules before solvating with water.
>
> -Nick
Sorry to interject myself into this discussion, but this is exactly what
packmol (
http://www.ime.unicamp.br/~martinez/packmol/) was written to
do. All you need is a pdb file for each of the components.
Bud Dodson
>
> On Jun 26, 2007, at 8:08 AM, David A. Case wrote:
>
>> On Thu, Jun 21, 2007, Nicolas Lux Fawzi wrote:
>>
>>> Could someone point me to a tutorial or any other info regarding
>>> setting up simulation system consisting of:
>>> multiple copies of short caped amino acids (ACE-X-NME) [ how do I get
>>> multiple copies of peptide in a system?
>>
>>> multiple copies of a GAFF/antechamber-built organic co-solvent built
>>> from a single pdb file
>>
>> The most straightforward approach would be to have a pdb file with
>> multiple
>> copies of the organic molecule, and then use the solvateBox or solvateOct
>> commands to add the water. But maybe I don't understand your question:
>> do you really have three components: some peptides, an (unspecified)
>> organic
>> solvent, and water?
>>
>> ....dac
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
--
M. L. Dodson
Email: mldodson-at-houston-dot-rr-dot-com
Phone: eight_three_two-56_three-386_one
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 27 2007 - 06:07:36 PDT
