[AMBER] Faulty_atom_connection error

From: nibedita jana <nibeditajana2015.gmail.com>
Date: Fri, 8 May 2015 15:36:02 +0530

Dear all
I am getting faulty atom connection error in tleap. I have cytochrome p450
with iron in complex with cysteine and a dioxy moiety bound to iron.
The commands I am using are
source leaprc.ff99SBildn
source leaprc.gaff
loadamberparams dioxy.frcmod
HEM = loadmol2 heme.mol2
CYP = loadmol2 cys.mol2
complex = loadpdb opt.pdb

*and the error is ERROR: Comparing atoms .R<HEM 497>.A<NB 24>,
        .R<HEM 497>.A<NA 18>, .R<HEM 497>.A<ND 9>, and
.R<HEM 497>.A<NC 1> to atoms .R<HEM 497>.A<NB 24>,
.R<HEM 497>.A<NA 18>, .R<HEM 497>.A<O1 74>, and .R<HEM
497>.A<NC 1> This error may be due to faulty Connection atoms.!FATAL
ERROR----------------------------------------!FATAL: In file
[chirality.c], line 142!FATAL: Message: Atom named O1 from HEM did not
match !!!ABORTING.*

I can understand this is a bond problem but I cannot figure it out.
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Received on Fri May 08 2015 - 03:30:02 PDT
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