Dear Francois,
Thanks a lot for your suggestion! The only thing is the Lys and the retinal
are connected by a Schiff base linkage rather than an amide bond, which
makes the capping of the retinal part tricky. But actually why do I need to
separate the residue into two fragments? I thought generating the charges
using the whole molecule should also work.
Regards,
Scarlett
On Mon, Dec 3, 2012 at 9:17 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Scarlett,
>
> You could use R.E.D. or R.E.D. Server...
>
> Split your whole molecule 'Lys-bound trans-retinal' into two capped
> building blocks.
> Then use charge constraints (intra-molecular charge constraints;
> intra-mcc) to remove these caps and generate the corresponding
> molecular fragments used to reconstruct your whole molecule connected
> (I guess) in a protein.
>
> ACE-NHCHCO-NME -> molecule 1; conformation(s) defined
> (CH2)4
> NH
> ACE
> 3 intra-mcc=0 on the 2 ACE & 1 NME capping groups
>
> trans_retinal_CO-NME -> molecule 2; conformation(s) defined
>
> 1 intra-mcc = 0 on the NME capping group
>
> R.E.D.
> ---> two fragments are generated
>
> NHCHCO -> fragment 1
> (CH2)4
> NH
>
> trans_retinal_CO -> fragment 2
>
> --->
>
> these fragments are associated in the LEaP program
>
> NHCHCO
> (CH2)4
> CO
> NH
> trans_retinal
>
> they are also connected in the protein...
>
> -AA(n-1)-NHCHCO-AA(n+1)-AA(n+2)-etc..
> (CH2)4
> CO
> NH
> trans_retinal
>
> I hope this helps.
>
> regards, Francois
>
>
> > Are there any "standard" Amber force field parameters for Lys-bound
> > cis-retinal and Lys-bound trans-retinal out there that people usually
> use?
> > (I only found
> >
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?ParameterTopologyRepository
> ,
> > but
> > it's for CHARMM and I assume the isomer should use a different set of
> > parameters.)
> >
> > If the answer is "no", could anyone give me a hint about how I can
> > construct one by my own?
>
>
>
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Received on Mon Dec 10 2012 - 04:30:02 PST
