Re: [AMBER] Regarding Antechamber Tutorial

From: sonali dhindwal <>
Date: Thu, 1 Jul 2010 14:13:05 +0530 (IST)

Hello Vaibhav,
Thanks for the reply.
I am getting the same result after using antechamber comand, that instead of mopac.out file, I am getting and sqm.out.
whereas in the tutorial it uses MOPAC but in sqm.out which I am getting uses AMBER SQM version and does QM calculation.
So its not the same which is mentioned in the tutorial, if that is the case with the different Amber version ? Because I am using amber11, whereas in tutorial it is amber10.
Sonali Dhindwal
--- On Thu, 1/7/10, vaibhav dixit <> wrote:
From: vaibhav dixit <>
Subject: Re: [AMBER] Regarding Antechamber Tutorial
To: "AMBER Mailing List" <>
Date: Thursday, 1 July, 2010, 1:19 PM
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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