Sirs and Madames:
I am having a confusion on Amber Tutorial B1. In the generation of the .prmtop file associated with vacuum DNA, I observe:
%VERSION VERSION_STAMP = V0001.000 DATE = 10/07/13 21:15:38
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
638 14 234 452 554 694 1162 1238 0 0
3544 20 452 694 1238 32 59 39 24 0
0 0 0 0 0 0 0 0 33 0
0
I have bolded the relevant number. The website lists the correct set of values as
638 14 234 452 554 694 1056 1238 0 0
3544 20 452 694 1238 32 59 39 24 0
0 0 0 0 0 0 0 0 33 0
0
The correct value is 1056, my value is 1162. My PDB file matches the website-posted pdb file. I am using ff99SB, which I believe is a unique specifier. Admittedly I am doing all of this through tleap, rather than following xleap in the tutorial, but this should not matter in principle.
Can anyone advise what mistake I am making that results in this difference?
Dr. Robert Molt Jr., Ph.D.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Mon Oct 07 2013 - 19:00:04 PDT
