Re: [AMBER] Regarding Antechamber Tutorial

From: vaibhav dixit <>
Date: Thu, 1 Jul 2010 13:19:30 +0530

Hi Sonali,
I had also faced similar problems with sustiva tutorial using amber10.
So I'm using a modified set of commands (in the attached file) to generate
.frcmod and .prepin files for the ligand and then load them before loading
the protein. This gives me .prmtop and .inpcrd files for the complex to
start my MD jobs.

I have used general terms like ligand, protein and complex in the file, just
to emphasize that it can be used for any ligand-protein combination and not
specific to sustiva case.

Regarding the paths I guess you will have to add them into your .bashrc and
source it before the changes take effect.

I guess this helps...

On Thu, Jul 1, 2010 at 12:53 PM, sonali dhindwal <> wrote:

> 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
> 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.out. and in terminal it is showing
> Running: /usr/local/amber11//bin/bondtype -j full -i
> Running: /usr/local/amber11//bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> Total number of electrons: 160; net charge: 0
> Running: /usr/local/amber11//bin/sqm -O -i -o sqm.out
> Running: /usr/local/amber11//bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> /usr/local/amber11//dat/antechamber/BCCPARM.DAT -s 2 -j 1
> Running: /usr/local/amber11//bin/atomtype -f ac -p bcc -o
> 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
> _______________________________________________
> AMBER mailing list

With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408

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Received on Thu Jul 01 2010 - 01:00:06 PDT
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