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)
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