[gmx-users] Re:gmx-users Digest, Vol 113, Issue 106

[aixintiankong]

Dear,
First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check  the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber  and then replace the AM1-BCC with the resp charge form    http://www.pharmacy.manchester.ac.uk/bryce/amber  . At last, i use "acpype –i ben.mol2 –c user" to get the nad.itp file.  
        so the NAD+ use the RESP charge and the ligand use the   AM1-BCC charges , can i do like this ?
        i use this method to get the NAD+.itp file? is correct or not ?






At 2013-09-24 02:24:20,gmx-users-request at gromacs.org wrote:
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>Today's Topics:
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>   1. Re: The charge of cofactor and ligand (Mark Abraham)
>   2. Re: Regarding g_sgangle index file (Teemu Murtola)
>   3. g_energy (Marcelo Vanean)
>   4. Re: confusion about implicint solvent (Szil?rd P?ll)
>   5. Re: Re: Charmm 36 forcefield with verlet cut-off scheme
>      (Justin Lemkul)
>   6. Re: script to convert the TIP3P water model into	TIP4(P)/2005
>      (Justin Lemkul)
>   7. Re: confusion about implicint solvent (Justin Lemkul)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 23 Sep 2013 19:40:23 +0200
>From: Mark Abraham <mark.j.abraham at gmail.com>
>Subject: Re: [gmx-users] The charge of cofactor and ligand
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
>	<CAMNuMAT5bsq5Xzr-q0zU27bt0hMA2m9wAuduF-6Lk+DN1SSYCA at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>How do GAFF and acpype work?
>
>Mark
>
>On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong <aixintiankong at 126.com> wrote:
>> Dear prof,
>> can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then  use acpype to  generate GAFF force field parameter for the NAD+ and ligand?
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