AMBER Archive (2007)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Mar 22 2007 - 16:11:07 CST

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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