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
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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address.
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Received on Fri Jun 03 2011 - 08:30:03 PDT
