AMBER Archive (2006)

Subject: AMBER: GLUTATHIONE

From: Joachim Reichelt (reichelt_at_gbf.de)
Date: Wed Jan 11 2006 - 08:40:30 CST

Dear all,

I want to model a structure with GLUTATHIONE.
I extracted the GTT-Lines from pdb1gsa.ent with grep an tried
to run antechamber. But all I get is:

Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C

I increase MAXVASTATE, but it did not help, so I set debug to 1.
Now I see:
...
double_a C1 0 0 0 0
double_a O11 0 0 0 0
double_a O12 0 0 0 0
double_a CB1 0 0 0 0
double_a CG1 0 0 0 0
double_a CD1 0 0 0 0
double_a OE1 0 0 0 0
double_a N2 0 0 0 0
double_a CA2 0 1 -4 -1
double_a C2 1 2 0 3
double_a O2 0 0 0 0
double_a CB2 0 0 0 0
double_a SG2 0 0 0 0
double_a N3 1 1 0 0
double_a CA3 0 0 0 0
double_a C3 0 0 0 0
double_a O31 0 0 0 0
double_a O32 0 0 0 0
double 11 CA2 C2 6
Cannot assign bond types for the current valence state

The current valence state (35) is listed as the following
...

More see in ant.log 

-- 
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         Joachim Reichelt

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