What a coincidence! I noticed the same issue today with a phosphorylated
serine (S2P). The 3 'free' oxygens bound to the phosphorus are O1P, O2P and
O3P (in the .off file
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/S2P.off and
thus also in the prmtop). ambpdb turns O1P into OP1 and O2P into OP2, but
leaves O3P as it is (and should be...)
Obviously, if you create your pdb with ptraj, you don't have this problem.
--Marc
On 3 June 2011 16:16, Brian Radak <radak004.umn.edu> wrote:
> 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
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Fri Jun 03 2011 - 09:00:04 PDT
