[AMBER] Regarding Antechamber Tutorial

From: sonali dhindwal <sonali11dhindwal.yahoo.co.in>
Date: Thu, 1 Jul 2010 12:53:09 +0530 (IST)

Hello All
I am new to Amber, I have installed amber 11 which is freely available,  on my linux system.
I tried to start with tutorial which is given at http://ambermd.org/tutorials/basic/tutorial4b/ for pharmaceutical ligands.
I gave first this command reduce sustiva.pdb > sustiva_h.pdb  to add hydrogens in the pdb file.
and then antechamber -i sustiva_new.pdb -fi pdb -o
sustiva.mol2 -fo mol2 -c bcc -s 2
but the output which is mentioned in tutorial is mopac.out file, instead I am getting is sqm.in, sqm.out. and in terminal it is showing
Running: /usr/local/amber11//bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /usr/local/amber11//bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 160; net charge: 0

Running: /usr/local/amber11//bin/sqm -O -i sqm.in -o sqm.out

Running: /usr/local/amber11//bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/local/amber11//dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /usr/local/amber11//bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
Why is this difference ?

and  also I am unable to set enviornment variable for the amber11 globally in the system, though I have mentioned it in csh.cshrc file at /etc/
setenv AMBERHOME /usr/local/amber11/
set path= ( $AMBERHOME/bin $path )

Everytime I have to use amber, i have to give these commands in the terminal. So what should I do such that i dont have to give these commands before use.

Any help regarding this will be highly appreciable.
Thanks in advance

Sonali Dhindwal
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Received on Thu Jul 01 2010 - 00:30:05 PDT
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