AMBER Archive (2007)

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

From: luckyang_at_gmail.com
Date: Thu Mar 22 2007 - 16:38:02 CST

I think you can simply draw a monomer structure of PEG in xleap and using
command "sequence" to generate a polymer. Here are the steps you can use as
a reference:

1, draw a monomer
2, set head, tail, connect0, connect1 of the monomer
3, generate oligomers with different length using "sequence" command
4, add H at two ends
5, using antechamber or R.E.D to obtain the partial charge for oligomers
(with different length to check the length effect)
6, modify the monomer atom type and partial charge based on result of
antechamber or R.E.D
7, generate the polymer using "sequence" and add the missing hydrogens.
8, modify the partial charge at two ends to neutralize the system.
9, save topology and coordinate files.
....
Hope this helps.

Lu Yang

On 3/22/07, Lili Peng <lilipeng_at_gmail.com> wrote:
>
> 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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>
>

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