[AMBER] unexpected behavior of ambpdb

From: Brian Radak <radak004.umn.edu>
Date: Fri, 3 Jun 2011 11:16:19 -0400

I'm aware that "expected behavior" is generally a matter of personal
preference, but I found the following to be odd when using ambpdb:

Using leap I defined a series of alkyl phosphate diester residues using what
I thought was a pretty standard naming convention for the atoms. Heres an
excerpt from one of my .off files:

 "O2'" "OH" 0 1 131075 7 8 -0.922500
 "O3'" "OS" 0 1 131075 8 8 -0.647500 <-- 1st bridge oxygen
 "P" "P" 0 1 131075 9 15 1.585600 <-- central phosphorus
 "O1P" "O2" 0 1 131075 10 8 -0.910000 <-- non-bridging oxygens
 "O2P" "O2" 0 1 131075 11 8 -0.910000
 "O5*" "OS" 0 1 131075 12 8 -0.629800 <-- 2nd bridge oxygen
 "C5*" "CT" 0 1 131075 13 6 -0.070000

My parm7s appear to build just fine without any errors. However, when I
minimized the structure and used ambpdb to visualize the output with VMD I
noticed that the non-bridge oxygens received inverted names:

O1P --> OP1
O2P --> OP2

This caused errors when I loaded the pdb back into leap in order to check
for close contacts. Did I violate some AMBER naming rule or is ambpdb just
being silly?

Brian

-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
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 Department of Chemistry                          :     Piscataway, NJ
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 radak004.umn.edu                                 :
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Received on Fri Jun 03 2011 - 08:30:03 PDT
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