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/
----- Original Message -----
From: "Julio Dominguez" <acheron24.hotmail.com>
To: amber.ambermd.org
Sent: Monday, August 19, 2013 5:43:52 AM
Subject: [AMBER] Two questions in one...
Hello AmberMDmen and women,
I have two different questions:
1) I have a few mdcrd files that I copied via sftp program that offers the option to "continue" or "append" files that have been previously downloaded. I think that this process corrupted a some of my files. They are still the right size but I can only read 86 frames out of 2500 or 1400 out of 2500. I no "original" for these files (yeah, entirely my fault). Is there anything I can attempt to recover them?
2) We are thinking about running some simulations with N-Acetylglucosamine 6-phosphate. The N-Acetylglucosamine can be easily build via Leap/Glycam but I am not sure about the phosphate. Due to the modular nature of the AMBERFF (and GAFF and GLYCAM) I wonder what would be the best approach to create the N-Acetylglucosamine 6-phosphate residue. Mostly, would it be necesary to parametrize N-Acetylglucosamine 6-phosphate via RED? Anybody has any experience with this type of sugars?
On a side note, in my group we are running AMBER on three GTX Titans. They have been humming along perfectly since the 325.15 driver update.
Best regards.
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Received on Mon Aug 19 2013 - 00:30:02 PDT
