AMBER Archive (2008)

Subject: Re: AMBER: using packmol file in Amber

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Mon Dec 15 2008 - 10:39:53 CST

Yes, you can use something like that.

I also attach here a simple awk script that also does the trick (for
me, at least). Notice that it is intended only as a MODEL for you, and
you will need to edit it for your specific case. You may want to
familiarize yourself with the sed and awk commands.

Good luck, 

--
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA

On Mon, Dec 15, 2008 at 10:57 AM, oguz gurbulak <gurbulakoguz_at_yahoo.com> wrote:
>
> Dear Prof. Case,
>
> I did all you suggested to me and I successfully got the input files. Thank
> you very much for your valuable information. I want to ask you some
> questions about adding TER cards and resp fitting . First, I 'm planning to
> study with 100 octane molecules. But it will be hard to add TER card
> manually into my packmol file. Can I add TER card with using a command or
> writing a script ? I found a link about it. Because of this reason I wanted
> to ask you about it. Could you help me about it?
>
> https://www.nbcr.net/pub/wiki/index.php?title=Relaxed_Complex_Scheme%2C_Part_I:_Molecular_Dynamics_and_Clustering#Add_TER_cards
>
> Secondly, I found a quick howto about resp fitting in Amber 8. I also
> attached this file to the mail. I want to ask you if I should do all the
> operations in quick howto file for getting prep and frcmod files for small
> organic molecules like n-alkanes. Or I should just do the operations below
> to get prep and frcmod files.
>
> Thanks in advance
>
> 1 antechamber -i n-octane.pdb -fi pdb -o octane_gin.gjf -fo gcrt
>
> 2 Run the gaussian.
>
> 3 antechamber -i octane_gin.out -fi gout -o octane.gaff.prep -fo prepi -nc 0
> -c resp -at gaff -rn OAS
>
> 4 parmchk -i octane.gaff.prep -f prepi -o octane.frcmod
>
> 5 antechamber -i octane.gaff.prep -fi prepi -o octane.gaff.pdb -fo pdb
>
> 6 use packmol with octane.gaff.pdb for getting 10 molecule ( added TER cards
> ) octane10.packmol.pdb file
>
> 7  xleap -s -f leaprc.gaff
>
> 8 loadAmberPrep octane.gaff.prep
>
> 9 loadamberparams octane.frcmod
>
> 10 octane = loadpdb octane10.packmol.pdb
>
> 11 check octane ( unit is OK )
>
> 12 saveamberparams octane octane10.prmtop octane10.inpcrd
>
> 13 Quit
>
> --- On Fri, 12/5/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:
>
> From: David A. Case <case_at_biomaps.rutgers.edu>
> Subject: Re: AMBER: using packmol file in Amber
> To: amber_at_scripps.edu
> Date: Friday, December 5, 2008, 9:58 AM
>
> On Fri, Dec 05, 2008, oguz gurbulak wrote:
>>
>> xleap -s -f leaprc.gaff
>> octane = loadpdb  octane.gaff.pdb
>> saveoff  octane  octane.lib
>> Quit
>
> This won't work at all.  The pdb file only has coordinates and atom/residue
> names in it; it doesn't have any atom types or charges that were generated
> by antechamber.
>
> You need to load the prepi file that antechamber created if you want to
> create
> a .lib file.  You don't really need the lib file here.  Load the prepi
> file,
> the frcmod file, and then the pdb file.  That way, leap has all
>  the information
> it should need.
>
>
> ....dac
>
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