Dear Scarlett,
> 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.
Yes you are right an imine
http://en.wikipedia.org/wiki/Schiff_base is
different from a peptide bond... this should be interesting to find a
way to split a whole molecule having an imine/Schiff base...
> 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.
See the abstract at
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
we tried to describe the advantages of the building block approach.
regards, Francois
> 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 Wed Dec 12 2012 - 22:30:04 PST
