---------------------------- Original Message ----------------------------
Subject: [Fwd: problem in bond connection]
From: "RINU
KHATTRI" <IBI2008024.iiita.ac.in>
Date: Tue, May 4, 2010
11:29
To: amber-owner.ambermd.org
--------------------------------------------------------------------------
---------------------------- Original Message
----------------------------
Subject: problem in bond connection
From: "RINU KHATTRI" <IBI2008024.iiita.ac.in>
Date: Tue, May 4, 2010 11:23
To: amber.ambermd.org
--------------------------------------------------------------------------
hello sir iam a student doing work on simulation
on
rnase using amber8
tool i hav eproblem in tleap program the
out put
given several error
during bond connect my input file
is file
obtained from modeller 9v7 tool
its an 1fs3 pdb id in
which one
peptide is removed an modelled the
structure the
error are
WARNING: The unperturbed charge of the unit:
6.000000 is not
zero.
Warning: Close contact of 1.655710
angstroms
between
.R<THR 3>.A<HG23 10> and
.R<ALA 5>.A<H
2>
Warning: Close contact of 0.807768 angstroms between .R<SER
14>.A<HB3 7> and .R<LEU 15>.A<H
2>
Warning: Close contact of 2.096464 angstroms between .R<CYX
20>.A<H 2> and .R<THR 93>.A<HG22
9>
Warning: Close contact of 1.649571 angstroms between .R<LYS
25>.A<HZ3 20> and .R<THR 30>.A<HB
6>
Warning: Close contact of 1.248436 angstroms between .R<ASN
28>.A<HD22 12> and .R<LYS 31>.A<HE2
15>
Warning: Close contact of 1.886384 angstroms between .R<LYS
31>.A<HZ1 18> and .R<LYS 31>.A<HB3
7>
Warning: Close contact of 1.586400 angstroms between .R<VAL
37>.A<HG23 14> and .R<ARG 79>.A<HD2
12>
Warning: Close contact of 2.206253 angstroms between .R<GLN
54>.A<HE21 14> and .R<SER 69>.A<HA
4>
Warning: Close contact of 2.001777 angstroms between .R<GLN
54>.A<HB3 7> and .R<LYS 55>.A<H
2>
Warning: Close contact of 2.068130 angstroms between .R<ASN
65>.A<HD21 11> and .R<ALA 103>.A<HB2
7>
Warning: Close contact of 1.917812 angstroms between .R<ILE
100
---------------------------- Original Message ----------------------------
Subject: problem in bond connection
From: "RINU KHATTRI" <IBI2008024.iiita.ac.in>
Date: Tue, May 4, 2010 11:23
To: amber.ambermd.org
--------------------------------------------------------------------------
hello sir iam a student doing work on simulation on rnase using amber8
tool i hav eproblem in tleap program the out put given several error
during bond connect my input file is file obtained from modeller 9v7 tool
its an 1fs3 pdb id in which one peptide is removed an modelled the
structure the error are
WARNING: The unperturbed charge of the unit:
6.000000 is not zero.
Warning: Close contact of 1.655710 angstroms
between .R<THR 3>.A<HG23 10> and .R<ALA 5>.A<H
2>
Warning: Close contact of 0.807768 angstroms between .R<SER
14>.A<HB3 7> and .R<LEU 15>.A<H
2>
Warning: Close contact of 2.096464 angstroms between .R<CYX
20>.A<H 2> and .R<THR 93>.A<HG22
9>
Warning: Close contact of 1.649571 angstroms between .R<LYS
25>.A<HZ3 20> and .R<THR 30>.A<HB
6>
Warning: Close contact of 1.248436 angstroms between .R<ASN
28>.A<HD22 12> and .R<LYS 31>.A<HE2
15>
Warning: Close contact of 1.886384 angstroms between .R<LYS
31>.A<HZ1 18> and .R<LYS 31>.A<HB3
7>
Warning: Close contact of 1.586400 angstroms between .R<VAL
37>.A<HG23 14> and .R<ARG 79>.A<HD2
12>
Warning: Close contact of 2.206253 angstroms between .R<GLN
54>.A<HE21 14> and .R<SER 69>.A<HA
4>
Warning: Close contact of 2.001777 angstroms between .R<GLN
54>.A<HB3 7> and .R<LYS 55>.A<H
2>
Warning: Close contact of 2.068130 angstroms between .R<ASN
65>.A<HD21 11> and .R<ALA 103>.A<HB2
7>
Warning: Close contact of 1.917812 angstroms between .R<ILE 100
hello sir iam a student doing work on simulation on rnase using amber8 tool
i hav eproblem in tleap program the out put given several error during bond
connect my input file is file obtained from modeller 9v7 tool its an 1fs3
pdb id in which one peptide is removed an modelled the structure the error
are
WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
Warning: Close contact of 1.655710 angstroms between .R<THR 3>.A<HG23 10>
and .R<ALA 5>.A<H
2>
Warning: Close contact of 0.807768 angstroms between .R<SER 14>.A<HB3 7> and
.R<LEU 15>.A<H
2>
Warning: Close contact of 2.096464 angstroms between .R<CYX 20>.A<H 2> and
.R<THR 93>.A<HG22
9>
Warning: Close contact of 1.649571 angstroms between .R<LYS 25>.A<HZ3 20>
and .R<THR 30>.A<HB
6>
Warning: Close contact of 1.248436 angstroms between .R<ASN 28>.A<HD22 12>
and .R<LYS 31>.A<HE2
15>
Warning: Close contact of 1.886384 angstroms between .R<LYS 31>.A<HZ1 18>
and .R<LYS 31>.A<HB3
7>
Warning: Close contact of 1.586400 angstroms between .R<VAL 37>.A<HG23 14>
and .R<ARG 79>.A<HD2
12>
Warning: Close contact of 2.206253 angstroms between .R<GLN 54>.A<HE21 14>
and .R<SER 69>.A<HA
4>
Warning: Close contact of 2.001777 angstroms between .R<GLN 54>.A<HB3 7> and
.R<LYS 55>.A<H
2>
Warning: Close contact of 2.068130 angstroms between .R<ASN 65>.A<HD21 11>
and .R<ALA 103>.A<HB2
7>
Warning: Close contact of 1.917812 angstroms between .R<ILE 100
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Received on Tue May 11 2010 - 06:00:03 PDT
