From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri May 02 2014 - 12:21:09 CDT
Actually, the CHARMM General Force Field (CGenFF), which is part of the
CHARMM force field, does support compounds with various degrees of
fluorination as encountered in drug-like molecules. While this doesn't
formally cover teflon polymers, their CGenFF representation cannot be too
terrible. If you want to simulate pure teflon (or possibly a teflon-water
interface), a materials force field may do better, but if you want to
study the interaction between teflon and a biomolecule represented by
CHARMM, you definitely need to use CGenFF for teflon.
CGenFF topology and parameter files for teflon can be built by analogy
from RESI TFE and RESI DFET in the main CGenFF topology file. (Rawan
didn't use CGenFF atom types and has horrible charges; fluorine is the
most electronegative element and does not behave like hydrogen.) A good
initial guess can be obtained from the CGenFF program at paramchem.org .
As an example, I attached a mol2 file for perfluorohexane and its
associated CGenFF-generated toppar stream file, and another one where I
manually adjusted the charges with the eye on constructing
arbitrary-length polymers. More information on the pertinent websites and
FAQs (you can find them easily using Google). Also vaguely related:
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=33766
On 05/02/2014 12:10 PM, Rawan Al Nsour wrote:
> I think it is doable
>
>
> On Fri, May 2, 2014 at 11:43 AM, Hongbo Du <hongbodu_at_uark.edu
> <mailto:hongbodu_at_uark.edu>> wrote:
>
> Hi, Rawan,
>
> I don't think the Charmm force field can work well with the Teflon
> long chain in my opinion because CHARMM was generated from protein and
> RNA, etc., not for amorphous materials. Please check the COMPASS force
> field available with Materials Studio. I am working on one material
> similar to Teflon with MS. At first you can try.
>
> Good luck.
>
> Hongbo
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> [owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf
> of Rawan Al Nsour [alnsourra_at_vcu.edu <mailto:alnsourra_at_vcu.edu>]
> Sent: Friday, May 02, 2014 9:57 AM
> To: namd-l
> Subject: namd-l: Teflon New Residue
>
> Dear All,
>
> I am working in teflon polymer long chain C200F402 . I derived the
> charges I need to build a new residue for CF3 and F3 as agroup and CF2
> anf F2 as a group, my question is CF3 is connected to CF2 and the
> latter is connected to rest of same CF2 in that long chain ending with
> CF3, is this residue representing this long chain?
>
> RESI AAA 0.00
> Group
> Atom C1 C3 -0.27 ! F11 F21
> Atom F11 F3 0.09 ! \ |
> Atom F12 F3 0.09 ! F12-C1-------C2--
> Atom F13 F3 0.09 ! / |
> Group F13 F22
> Atom C2 C2 -0.18
> Atom F21 F2 0.09
> Atom F22 F2 0.09
>
> Thanks,
> Rawan
>
>
>
> --
> Rawan Al Nsour
> Ph.D. Candidate
> Department of Mechanical and Nuclear Engineering
> School of Engineering, Virginia Commonwealth University
> E-mail: alnsourra_at_vcu.edu
> <mailto:alnsourra_at_vcu.edu><mailto:alnsourra_at_vcu.edu
> <mailto:alnsourra_at_vcu.edu>>
> 401 W. Main Street, Room E3216
> P.O. Box 843015
> Richmond, Virginia 23284-3015
>
>
>
>
>
>
>
>
>
>
> --
> Rawan Al Nsour
> Ph.D. Candidate
> Department of Mechanical and Nuclear Engineering
> School of Engineering, Virginia Commonwealth University
> E-mail: alnsourra_at_vcu.edu <mailto:alnsourra_at_vcu.edu>
> 401 W. Main Street, Room E3216
> P.O. Box 843015
> Richmond, Virginia 23284-3015
>
>
>
>
>
>
>
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