[Fwd: Problems with heteroatoms (Zn)]
Hi, I have this problem solved. I had a wrong representation of the Zn heteroatoms in my PDB file. It had to be annotated as ZN2 and not ZN, because that's how it's represented in the top_heav.lib file. Thanks to one of the modeller users who pointed this out to me - I'm sorry I forget his name.
Regards, Sirisha Sunkara
hello all,
I want to build an all hydrogen atom model with a heme group. I already set the /scripts/__defs.top as follows as described in FAQ 15: SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on SET TOPOLOGY_LIBRARY = $(LIB)/top.lib SET PARAMETERS_LIBRARY = $(LIB)/par.lib and the alignment.ali file is as: >P1;1fdx structureX:1fdx:1:@:105:@:ferredoxin:Peptococcus aerogenes: 2.00:-1.00 GDIEKGKKIFVQKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLENPKKY IPGTKMIFAGIKKKAERADLIAYLKQATAEh*, in which the last residue h is the heme group. I use the pdb file from protein databank and put HEME for the heme group in the pdb file. but I kept on having problems and no output with heme group and hydrogen.. the error message in the model-default.log file is,
iup2crm_E> IUPAC atom not found in topology library: DD1 csrrng__E> atom index out of bounds: 808 Possible reasons: missing SET HETATM_IO = on missing SET WATER_IO = on missing SET HYDROGEN_IO = on
any suggestions? thanks a lot.
Yan
******************************************** Yan Yao 157 Colburn Lab. Department of Chemical Engineering University of Delaware Newark, DE 19716 Tel: (302)831-6314(O) ********************************************
participants (2)
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Sirisha sunkara -
Yan Yao