AMBER Archive (2009)

Subject: RE: [AMBER] Tutorial 4 Parameter file was not saved

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 27 2009 - 12:31:30 CDT

Hi Workalemahu,

This is your problem:

" TUTORIAL B4: Simulating a pharmaceutical compound using antechamber and
the Generalized Amber Force Field. (Updated for AMBER 10 and AMBERTools
1.2)"

I updated it to match AMBERTools 1.2. You can either download AMBERTools 1.2
for free (from http://ambermd.org/) or you can use this page
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/ which I
believe is still for AMBER 9.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Workalemhu Berhanu
> Sent: Wednesday, May 27, 2009 9:01 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] Tutorial 4 Parameter file was not saved
>
> Dear all
> I am new to amber and I am doing tutorial 4 with amber9. I followed all
> the steps as mentioned in the tutorial.
> I when I put the command $AMBERHOME/exe/antechamber -i sustiva.pdb -fi
> pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
> ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_AC.AC0
> ANTECHAMBER_AC.A divcon.in divcon.out ANTECHAMBER_AM1BCC_PRE.AC
> ANTECHAMBER_AM1BCC.AC ATOMTYPE.INF sustiva.pdb sustiva.mol2
> There is file no file written my directory with the following names
> divicon.pdb mopac.in mopac.out mopac.pdb
> Ignoring this I when with the remaining steps in the tutorial and I
> used the parmchk utility and then put the command
> $AMBERHOME/exe/parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
> A file called sustiva.frcmode was produced. I opened xleap loaded it
> with sustiva.mol2checked SUS and opened and closed the edit widow . I
> put the commanded
> loadamberparams sustiva.frcmod
> to tell the xleap the parameter for missing angle types
> but when check out the SUS unit again there is still a missing angle
> parameter and I could not get the prmtop and inpcrd files
>
> Is it because I am using amber9? Can anyone tell me what do?
>
> Thank you
> Workalemahu
>
>
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