ADL: Parameters for phosphorus atoms?

SRMD, Col - Platt, Steven Steven.Platt at hpa.org.uk
Thu Feb 10 08:13:40 PST 2005


Dear List,
 
I'm reading in a protein/DNA complex (MOL" format) as a static
macromolecule, with the aim of creating a grid, etc... but ADT comes up with
the error 
"macromolecule has an unusual atom type: P
Do you want to add this type which means changing 
P to M and defining new energy parameters?"
 
This brings up 2 questions...
1)       I thought AutoDock recognised P (phosphorus) as a legitimate atom
type. Is this not the case?
2)       What are correct parameters (Rij & epsij) for Phosphorus?
http://www.scripps.edu/mb/olson/gmm/autodock/ad305/Using_AutoDock_305.21.htm
l
<http://www.scripps.edu/mb/olson/gmm/autodock/ad305/Using_AutoDock_305.21.ht
ml>  suggests that "a very rough approximation for phosphorus parameters is
to borrow those of carbon"... where would a novice like myself find this
information?
 
Many thanks
 
Steve
 
Steve Platt
Bioinformatics Support Co-ordinator
Genomics, Proteomics & Bioinformatics Unit
HPA Colindale
61 Colindale Avenue
London
UK
NW9 5HT
http://www.hpa.org.uk/srmd/bioinformatics/index.htm
<http://www.hpa.org.uk/srmd/bioinformatics/index.htm> 
 



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