Subject: Re: DGEOM questions for conf anal...

From: <[email-masked]>
Date: Wed, 17 Nov 93 23:40:12 -0500

Hi Joe-
The issue of flat phenyl rings in DGEOM comes up from time to time.  Generally,
distance constraints alone are not enough to keep things from having some
pucker.  This is basically because it doesn't take a very big distance
bounds violation to give noticable deviations from planarity.  DGEOM will
put chiral constraints on phenyl rings with a chiral volume of zero which
tends to keep them much flatter.  However, it will only do this if you have
provided bond order information in the input PDB file.  You need to indicate
a Kekule (alternating single and double bond) structure for the phenyl rings.
This is done with a non-standard extension to the PDB format (to indicate
double bonds, you put the connected atoms numbers in twice in the CONECT
record, ie, if atom 6 is doubly bonded to atom 5 the record would look
like CONECT    6    5     5).  If you are doing that and the phenyl rings
are still noticably non-planar, then there is something wrong and you should
give me more details.
Hope this helps.
Scott Dixon ([email-masked])