AMBER Archive (2007)

Subject: Re: AMBER: Generating structure of polyethylene glycol in AMBER

From: Lili Peng (lilipeng_at_gmail.com)
Date: Thu Mar 22 2007 - 16:17:22 CST

Francois - thank you for your quick reply. I will look into it.

On a side note, I was also told that I could use Accelrys' Discovery Viewer
software to draw the PEG structure. Do you know if that program allows me to
generate a file in a format that can be accessed by VMD?

Thanks in advance.
Lili

On 3/22/07, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
> Quoting Lili Peng <lilipeng_at_gmail.com>:
>
> >> I am new to AMBER, and I would like to know what is the best way to
> > generate
> >> a structure of polyethylene glycol (PEG) in AMBER. Should I compose a
> > prep
> >> file and process it in xleap or antechamber and then generate a PDB
> file?
> > Any guidance
> >> would be greatly appreciated.
>
> You can also use R.E.D. http://q4md-forcefieldtools.org/RED/ to derive
> RESP charge values & generate a Tripos mol2 file as a precursor of a
> FF library...
>
> Exemple of many R.E.D. jobs are available in R.E.D.D.B.
> See of instance the W-46 & W-79 R.E.DD.B. projects
> http://q4md-forcefieldtools.org/REDDB/up/W-46/
> http://q4md-forcefieldtools.org/REDDB/up/W-79/
>
> regards, Francois
>
>
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