Re: Patch to connect monomers code

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue May 06 2014 - 13:33:49 CDT

You're on the right track, but I would use a RESI for the "bulk polymer"
and a PRES for the termini, like this:

RESI TEFL 0.00
GROUP
ATOM C CG312 0.38
ATOM F1 FGA2 -0.19
ATOM F2 FGA2 -0.19

BOND C F1 C F2
BOND C -C C +C ! bonds to previous and next monomer

PATCh FIRST TEFT LAST TEFT ! default capping patches; see below

PRES TEFT 0.38
ATOM C CG312 0.44 ! change the charge on existing atom
ATOM C0 CG302 0.36 ! add an extra methyl group
ATOM F01 FGA3 -0.14
ATOM F02 FGA3 -0.14
ATOM F03 FGA3 -0.14

BOND C C0 C0 F03 ! bonds for extra methyl group
BOND C0 F02 C0 F01

And then you can generate your polymer just like a biopolymer; in the
CHARMM program, that would be:
READ SEQUence TEFL 62
GENErate TEF FIRST TEFT LAST TEFT SETUp WARN
but I'm not sure what the equivalent is for psfgen or VMD.

Note that I didn't include IC tables in my RESI or PRES, so I'm assuming
you're using a program/procedure that doesn't rely on them. In case you do
need them, I don't think it is possible to construct a valid IC table for
a one-atom monomer, so you'd need to make your monomer 2 carbons long.

On 05/06/2014 10:05 AM, Rawan Al Nsour wrote:
> Dear Dr. Kenno,
> Thank you and yes that is what I need. However, I just need more
> clarification to make sure that I am on the right path.
> for example I have long teflon chain C64F130
>
> I need to produce chain that is three times longer (polymer) so patch
> should be ??
> F
> I
> -----C------
> I
> F
>
> the patch command is there more clarfication for example my pdb name or
> residue TEFL so is it to make the three units
>
> patch TEFL TEFL TEFL
>
> Thank you,
>
>
> On Mon, May 5, 2014 at 12:50 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> From your previous post, it looks like you might really be looking
> for how to construct a residue that can be polymerized up to arbitrary
> length and capped at the ends. If so, look at RESI PEGM and the
> associated PRES termini in the CGenFF main file. A polymer is
> generated just like biopolymers. I hope this answers your question; if
> not, clarify.
>
>
> On 05/04/2014 01:15 PM, Rawan Al Nsour wrote:
>
> Dear All,
> Is there a an clear and detailed example of a code that represents
> using a
> patch to connect two monomers or more.
>
> 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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