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 Sat Nov 12 2011 - 10:30:02 PST
