[AMBER] COOH group:extra undesired bond::NO reply :-(

From: Jio M <jiomm.yahoo.com>
Date: Fri, 2 Apr 2010 23:34:45 -0700 (PDT)

Dear Amber users,

I had same problem before also, subject being: "COOH group troubling"

Now I have different molecule, whose N is to be further attached to
other residues and then minimisation. But the COOH is showing undesired bond while doing
minimisation. The RESP charges were derived. The bond is between C of
carbonyl and H of OH. So a sort of triangle being formed.

FILE CONTAINS FOUR MOL2 files for same molcule

for *_all.mol2 : IOp(6/33=2,6/41=10,6/42=17) was used as in tutorial

 for *.mol2: IOp(6/33=2) was used

--COCH3 was removed before joining to other reisdue
It could be a visualiser problem, but minimisation is not getting
completed because 1-4 EEL is going like **************. So I think it
is not a visualiser problem, because similar problem was there in COOH
of bengal rose ("COOH group troubling"). This was suggested and solved by Dr. Junmei
Wang as he provided charges using CEP-121g.
Now in new case (attached files) I tried with CEP121g basis set also and HF631G but in
both cases a triangle is formed in minimisation step after joining it to other residue. Please suggest what can be the
problem and its remedy too.
thanks for your patience

thanks and regards,



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Received on Sat Apr 03 2010 - 00:00:03 PDT
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