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 03 2012 - 21:30:02 PST
