Dear Changwoo Do,
You might use R.E.D. Server .
http://q4md-forcefieldtools.org/ to
build your oligo/polymer. You need to start from whole
molecule(s)/elementary building block(s) and define specific charge
constraints during the fitting step to create the required molecular
fragment(s) to be oligo/polymerized.
You can find many examples of polymer building .
http://q4md-forcefieldtools.org/Tutorial/
regards, Francois
> Hi,
>
> I wanted to build a long polymer chain. Here are the steps I tried.
>
> [First], I have created, a monomer, styrene sulfonate.
>
> CH2-CH
> |(connects to CH)
> AR
> |
> SO3(-)
>
> Using xleap, I connected tail of the first monomer (CH) to the head of
> the second monomer (CH2) and save it as mol2 file. And I tried to run
> antechamber as follows,
>
> ===copy from here===
> $ antechamber -i ss2.mol2 -fi mol2 -o ss2c.mol2 -fo mol2 -c bcc -j 4
> -s 2 -nc -2
> Running: /home/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> ---Judge bond type for Residue 1 with ID of 1 and Name of SSM ---
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will
> significantly increase the computation time
>
> Error: cannot run "/home/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
> ===paste ends here===
>
> so it wasn't successful.
>
> [Second], I ran 'antechamber' on a single monomer (described above).
> It went through with option [-nc -1] since the net charge is not zero
> due to SO3-. However, after this antechamber, the bond assignment has
> been changed to: (single to double bond between CH2 anc CH)
>
> CH2=CH
> |(connects to CH)
> AR
> |
> SO3(-)
>
> Well, I was able to connect two or more of this monomers to create
> longer chains. But this double bond won't change, which is
> unrealistic. And now I'm stuck..
>
>
> [Ultimate goal]. In any way, my ultimate goal is to create a polymer,
> which looks as follows:
>
> ENDGROUP -(CH2-CH)-(CH2-CH)-...-(CH2-CH)-ENDGROUP
>
> Obvious, if I create a long chain polymer, then antechamber won't
> work, because there are too many atoms. Then, how can I build a
> polymer and assign charges and forcefields to this polymer.
>
> Thank you for your helps.
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Received on Tue Nov 15 2011 - 04:30:04 PST
