Hi mi name is Alex Rendon , im working on a protein/DNA complex,
i´m following tutorial 2
Using dynamics simulations to estimate binding
energetics<
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_two/>
,
i can save the prmtom and inpcrd files only from the protein alone
the problem is DNA because atoms 212, 217 and 222 does not have a type, i
have already read the pdb but i cannot find what is the problem with my
file, i hope you can help, im using amber 12 for Mac Lion 10.8.3 thank for
your help
so i have already set path to amber
N-terminal:amber javieralejandrorendoncarrillo$ export
AMBERHOME=/Users/javieralejandrorendoncarrillo/amber/amber12
run parametrization of ligand in file directory
N-terminal:amber javieralejandrorendoncarrillo$ $AMBERHOME/bin/tleap -s -f
$AMBERHOME/dat/leap/cmd/leaprc.ff99SB
then i load the pdb of the protein and DNA
> complex = loadpdb complex.pdb
Loading PDB file: ./complex.pdb
and also the DNA pdb alone
> ADN = loadpdb ADN.pdb
Loading PDB file: ./ADN.pdb
> check ADN
Checking 'ADN'....
saveAmberParm ADN ADN.prmtop ADN.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -44.000000 is not zero.
FATAL: Atom .R<T 212>.A<P 1> does not have a type.
FATAL: Atom .R<T 212>.A<O1P 2> does not have a type.
FATAL: Atom .R<T 212>.A<O2P 3> does not have a type.
FATAL: Atom .R<T 212>.A<O5' 4> does not have a type.
FATAL: Atom .R<T 212>.A<C5' 5> does not have a type.
FATAL: Atom .R<T 212>.A<C4' 6> does not have a type.
FATAL: Atom .R<T 212>.A<O4' 7> does not have a type.
FATAL: Atom .R<T 212>.A<C3' 8> does not have a type.
FATAL: Atom .R<T 212>.A<O3' 9> does not have a type.
FATAL: Atom .R<T 212>.A<C2' 10> does not have a type.
FATAL: Atom .R<T 212>.A<C1' 11> does not have a type.
FATAL: Atom .R<T 212>.A<N1 12> does not have a type.
FATAL: Atom .R<T 212>.A<C2 13> does not have a type.
FATAL: Atom .R<T 212>.A<O2 14> does not have a type.
FATAL: Atom .R<T 212>.A<N3 15> does not have a type.
FATAL: Atom .R<T 212>.A<C4 16> does not have a type.
FATAL: Atom .R<T 212>.A<O4 17> does not have a type.
FATAL: Atom .R<T 212>.A<C5 18> does not have a type.
FATAL: Atom .R<T 212>.A<C5M 19> does not have a type.
FATAL: Atom .R<T 212>.A<C6 20> does not have a type.
FATAL: Atom .R<T 217>.A<P 1> does not have a type.
FATAL: Atom .R<T 217>.A<O1P 2> does not have a type.
FATAL: Atom .R<T 217>.A<O2P 3> does not have a type.
FATAL: Atom .R<T 217>.A<O5' 4> does not have a type.
FATAL: Atom .R<T 217>.A<C5' 5> does not have a type.
FATAL: Atom .R<T 217>.A<C4' 6> does not have a type.
FATAL: Atom .R<T 217>.A<O4' 7> does not have a type.
FATAL: Atom .R<T 217>.A<C3' 8> does not have a type.
FATAL: Atom .R<T 217>.A<O3' 9> does not have a type.
FATAL: Atom .R<T 217>.A<C2' 10> does not have a type.
FATAL: Atom .R<T 217>.A<C1' 11> does not have a type.
FATAL: Atom .R<T 217>.A<N1 12> does not have a type.
FATAL: Atom .R<T 217>.A<C2 13> does not have a type.
FATAL: Atom .R<T 217>.A<O2 14> does not have a type.
FATAL: Atom .R<T 217>.A<N3 15> does not have a type.
FATAL: Atom .R<T 217>.A<C4 16> does not have a type.
FATAL: Atom .R<T 217>.A<O4 17> does not have a type.
FATAL: Atom .R<T 217>.A<C5 18> does not have a type.
FATAL: Atom .R<T 217>.A<C5M 19> does not have a type.
FATAL: Atom .R<T 217>.A<C6 20> does not have a type.
FATAL: Atom .R<T 222>.A<P 1> does not have a type.
FATAL: Atom .R<T 222>.A<O1P 2> does not have a type.
FATAL: Atom .R<T 222>.A<O2P 3> does not have a type.
FATAL: Atom .R<T 222>.A<O5' 4> does not have a type.
FATAL: Atom .R<T 222>.A<C5' 5> does not have a type.
FATAL: Atom .R<T 222>.A<C4' 6> does not have a type.
FATAL: Atom .R<T 222>.A<O4' 7> does not have a type.
FATAL: Atom .R<T 222>.A<C3' 8> does not have a type.
FATAL: Atom .R<T 222>.A<O3' 9> does not have a type.
FATAL: Atom .R<T 222>.A<C2' 10> does not have a type.
FATAL: Atom .R<T 222>.A<C1' 11> does not have a type.
FATAL: Atom .R<T 222>.A<N1 12> does not have a type.
FATAL: Atom .R<T 222>.A<C2 13> does not have a type.
FATAL: Atom .R<T 222>.A<O2 14> does not have a type.
FATAL: Atom .R<T 222>.A<N3 15> does not have a type.
FATAL: Atom .R<T 222>.A<C4 16> does not have a type.
FATAL: Atom .R<T 222>.A<O4 17> does not have a type.
FATAL: Atom .R<T 222>.A<C5 18> does not have a type.
FATAL: Atom .R<T 222>.A<C5M 19> does not have a type.
FATAL: Atom .R<T 222>.A<C6 20> does not have a type.
Failed to generate parameters
Parameter file was not saved.
--
LBG Javier Alejandro Rendón Carrillo
Laboratorio de Investigación y Desarrollo
Tel. (044) 81-80-52-05-76
El control del espacio y el estricto manejo
del tiempo son factores determinantes
para aquellas personas que pretendan
alcanzar y sostener un desempeño
eficiente.
CONTROL DEL ESPACIO: Orden en las
cosas, en los archivos y en los registros.
ESTRICTO MANEJO DEL TIEMPO: Ser
puntual y saber fijar prioridades y
cantidades de tiempo
M. Kant
Año-1780
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Received on Mon Apr 15 2013 - 14:30:03 PDT
