Re: [AMBER] Converting Amoeba .xyz for use with Amber

From: Eugene Yedvabny <eyedvabny.berkeley.edu>
Date: Mon, 9 Dec 2013 14:27:38 -0800

I am attaching my test files for your reference. The oxy_stripped.pdb is what was generated with cpptraj and oxy.pdb is my edited version with NHE -> NH2. You would need to change the path in the key file to point to your install of Tinker, but everything else should be generic.

Thank you,
Eugene Yedvabny
From: Eugene Yedvabny Eugene Yedvabny
Reply: Eugene Yedvabny eyedvabny.berkeley.edu
Date: December 9, 2013 at 2:24:39 PM
To: amber.ambermd.org amber.ambermd.org
Subject:  Converting Amoeba .xyz for use with Amber
Hello Dr. Case and Dr. Swails,

Sorry for the out-of-order reply; my mailing-list subscription was apparently disabled and I can't seem to directly reply to your responses.

I've sort-of figured out the root of my issue, but now am stuck on how to best resolve it. My Amoeba simulation was run on Oxytocin, built with AmberTool 13 tleap. Oxytocin is a capped protein with the NHE group as the 10th residue. Tinker, however, doesn't understand the NHE code and so I manually changed the residue code to NH2 in the pdb I generated with cpptraj. This made the pdb recognizable to Tinker's pdbxyz and analyze, but clearly screws something up with respect to tinker_to_amber reading the resulting analout (the numf=5 error). I also have a disulfide bridge between residues 1 and 6, but since both Amber and Tinker support CYS/CYX codes and bridge-making, I don't imagine that being the problem.

I've ran all the steps with a tleap-modeled Bradykinin and was able to generate working prmtop + inpcrd with Tinker 6.2 and Amber 12's tinker_to_amber. So I think the issue has to do with my NHE -> NH2 mod.

I am sure I am not the first person to attempt running capped peptides in Tinker, and yet I can't seem to find what others have done with respect to Tinker's handling of NHE/NH2. Have you come across this issue before, and if so, what would be the best resolution?

Thank you,
Eugene Yedvabny

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Received on Mon Dec 09 2013 - 15:00:02 PST
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