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-- 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.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.biomaps.rutgers.edu> wrote: > > From: David A. Case <case.biomaps.rutgers.edu> > Subject: Re: AMBER: using packmol file in Amber > To: amber.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 > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" (in the *body* of the email) > to majordomo.scripps.edu > >