[AMBER] COOH group:extra undesired bond

From: Jio M <jiomm.yahoo.com>
Date: Wed, 31 Mar 2010 09:41:06 -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.

(ATTACHED
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,



JIomm




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Received on Wed Mar 31 2010 - 10:00:02 PDT
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