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-requ...@gromacs.org wrote: >Send gmx-users mailing list submissions to > gmx-users@gromacs.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > >You can reach the person managing the list at > gmx-users-ow...@gromacs.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-users digest..." > > >Today's Topics: > > 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.abra...@gmail.com> >Subject: Re: [gmx-users] The charge of cofactor and ligand >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: > <camnumat5bsq5xzr-q0zu27bt0hma2m9wauduf-6lk+dn1ss...@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 <aixintiank...@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? >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >------------------------------
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