Hi,
On Sun, Aug 18, 2013 at 9:43 PM, Julio Dominguez <acheron24.hotmail.com> wrote:
> 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?
Unfortunately once a trajectory is corrupted that data is gone. ASCII
trajectories are particularly vulnerable because if a frame becomes
corrupted it is very difficult recover subsequent frames. With NetCDF
files the data is organized better so corrupted frames tend not to
affect good frames (unless the header somehow becomes corrupt in which
case you're toast).
When I'm transferring very large trajectories these days I've taken to
running md5sum on the original and comparing it to the copy. Some file
transfer protocols will do something like this for you but I like to
double check.
-Dan
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 19 2013 - 13:30:03 PDT
