Dear all
is there some one who have experience on Distance Restraint?
I want to restraint O atom in Ligand (MOL) and H atom in Protein at the beginning of minimization.
I edit a 7-col file res.upb.
179 MOL O3 86 LEU H 2.7
I extract coordinate of those two atom as res.pdb
ATOM 1364 H LEU 86 x y z
ATOM 2691 O3 MOL 179 x y z
then I use following command
makeDIST_RST -upb res.upb -pdb res.pdb -rst res.rst
the system give me ERROR information:
#makeDIST_RST
Currently configured for up tp 1000 atoms
Using MAP file /$AMBERHOME/dat/map.DG-AMBER
ERROR no map funciont for O3 MOL : data= 179 MOL O3 86 LEU H 2.7
Should I modify some content in map.DG-AMBER
I also want to restraint the distance of N on HIS and metal ions Zn2+
when I prepare the frcmod and prep file of ZN2+, I use Zn as atom name and ZNA as residue name.
I browsed the map.DG-AMBER file and found that ZN2+ is represented by ZN.
What should I modify to let my restraint success.
any suggestions would be very appreciated.
Best regard!
Y. Xu
yxu.mail.sioc.ac.cn
2005-04-08
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* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
* Email: yxu.mail.sioc.ac.cn
* xuyongch.yahoo.com
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Received on Fri Apr 08 2005 - 03:53:00 PDT
