AMBER Archive (2006)

Subject: AMBER: check as error: load prepin in tleap

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Fri May 26 2006 - 12:13:41 CDT

Dear CSML members
My idea is to generate prepin and frcmod for deprotonated tyrosine(TYR) and
lysine(LYS) by using RESP charge fitting derived from Gaussian03(G03). Now,
I can obtain charge from G03 (*.out) and also prepin and frcmod which were
used in Tleap. But the frcmod file seem not to be ok. So, I decide to check
frcmod again by using gasteiger charge in Antechamber.While I am trying to
load these files by edit name of LYS residue in enzyme pdb file to LYD (mean
deprotonated lysine), I found the errors occuring when every time I do
"check as" in Tleap and the result was also attacted here. That you can also
see the unbonded lysine which should be the peptide bond between GLY179 and
ASP181. How to link these bonds ? or May I do something wrong ?

Please tell me what I should do....

,Thanks

Jitrayut Jitonnom


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