Thanks Ben,
>> I believe that this carbon is usually in the R configuration
Yes I always see them to be R (text books, charmm gui; though I never found original paper who discovered it to be R :-) but never saw it to be S.
>> And, I don't know the structural details of the simulations in that paper.
Yes it was "S" in the simulation, as per the structure provided
Someone please clarify this following issue also, I mailed earlier.
>I am confused about the term "equivalent" and new for me. If it is the case
>then atom type like p5 (which I think was suitable instead of p4) will loose
>its significance to exist even!. lets say what gaff provides "p5 Phosphate
>with four connected atoms, such as O=P(OH)3". here also one can see three
>OHs being "equivalent", then can I say that atom type p2 is also OK or
>something like that.
________________________________
From: Benjamin Madej <bmadej.ucsd.edu>
To: 'AMBER Mailing List' <amber.ambermd.org>
Sent: Tuesday, July 17, 2012 3:24 AM
Subject: Re: [AMBER] lipid params
1. See my previous email. DMPC =
1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine. Myristoyl was not included in
Lipid11, but it'll probably be added in the future.
2. I made a mistake in the previous email and let me clarify: I meant to say
sn-2 carbon is the stereogenic center of the phospholipid (same carbon as in
your figure). I believe that this carbon is usually in the R configuration
according to the textbook I previously referenced. I haven't looked at other
sources in detail, though. And, I don't know the structural details of the
simulations in that paper.
Ben Madej
Walker Molecular Dynamics Lab
2) *** Prof./Dr. Benjamin,
>>I assume you're talking about the stereogenic center of the
>>phospholipid
To avoid further confusion, I have attached the image (source: JCC,29(1),
24-37). I was discussing about the boxed carbon C3 (it is DMPC molecule). No
other chiral centre I can see (please correct me).
It should be 'R' as what CHARMM GUI provides us but 'S' was used in
mentioned paper. Is there any special reason to use S and its validation
with GAFF?
3) *** Prof. Junmie Wang (gaff developer), Gould,
>>The P4 is correct, the phosphorous has three different substituents
attached, the two oxygens which are >> attached to the phosphorous are
equivalent.
I am confused about the term "equivalent" and new for me. If it is the case
then atom type like p5 (which I think was suitable instead of p4) will loose
its significance to exist even!. lets say what gaff provides "p5 Phosphate
with four connected atoms, such as O=P(OH)3". here also one can see three
OHs being "equivalent", then can I say that atom type p2 is also OK or
something like that.
thanks and regards,
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Received on Tue Jul 17 2012 - 03:30:02 PDT
