Hello Julio,
Could you tell me the charge state of the phosphate that you want to generate parameters for? This will be important for what molecules I upload.
Best regards,
Karl
----- Original Message -----
From: "Julio Dominguez" <acheron24.hotmail.com>
To: amber.ambermd.org
Sent: Wednesday, August 21, 2013 4:12:18 AM
Subject: Re: [AMBER] AMBER Digest, Vol 587, Issue 1
Hello Karl,
Thanks for your suggestions. I will go the RED way and also use Wolf2Pack. Thus, I'll appreciate it if you upload those phosphate containing molecules you mention to Wolf2Pack.
Best regards.
Hello Julio,
I can help answer your second question. You could do one of two approaches for generating N-Acetylglucosamine 6-phosphate's partial atomic charges. I would recommend using R.E.D. for both approaches. The more rigorous way would be to generate 3 to 4 representative conformations (e.g. omega-angle's gt, tg, and gg conformations), perform the QM minimizations, and then generate the corresponding MEP. The quicker way would be to generate charges for just the phosphate group (i.e. -PO3Hn), since Glycam contains an N-Acetylglucosamine group with an open valence at the O6 position. RED can also enable you to do this by modeling CH3O-PO3Hn as a representative molecule. I would consider both approaches acceptable, with the second approach being more generalizable for adding the phosphate group to other carbohydrates.
However, you may also need to check, validate, or develop bonded parameters for your molecule. You can use Wolf2Pack for this, which contains Glycam06, parm99SB, and gaff force fields. The website contains tutorials for how to check and optimize bond, angle and torsion parameters. Please post any questions regarding Wolf2Pack to its Message Board. Note, if you decide to do this I may have to upload some phosphate containing molecules for you - just let me know.
One last consideration is the charge state of the phosphate group. You will need to decide what pH you want to run your simulation at, and then develop the residue accordingly.
Best regards,
Karl
www.wolf2pack.com
http://q4md-forcefieldtools.org/RED/
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Received on Wed Aug 21 2013 - 01:00:04 PDT
