Thank you. I wanna know of the alternative method to carry out this simulation. other than using charmm gui. thank you
On Fri, Aug 10, 2018 at 2:07 PM, Abhishek Acharya <abhi117acha...@gmail.com> wrote: > I see. I have not used charmm-gui for building system as complex as yours, > so I can't comment on the issue. But this is a problem specific to > charmm-gui. I suggest you contact the authors of the web-service directly. > > Abhishek > > On Fri, Aug 10, 2018 at 10:07 AM, RAHUL SURESH <drrahulsur...@gmail.com> > wrote: > > > Hi. > > > > Thank you. > > > > But the system (protein ligand) is being constructed in charm gui input > > generator, where it automatically compare the complex pdb and ligand mol2 > > file ( which will Ben uploaded ). > > > > On Thu, 9 Aug 2018 at 11:24 PM, Abhishek Acharya < > abhi117acha...@gmail.com > > > > > wrote: > > > > > Hi, > > > > > > > > > > > > > It look so complicated to carry out a protein ligand simulation in > > Lipid > > > > bilayer system using charmm ff. I have a ligand with 27 atoms ( > > includes > > > > Hydrogen ). The initial structure (monomer) is simulated in popc > > > > constructed using charmm gui web page. To construct the same for the > > > > portein-ligand complex is too tedious and very problematic. > > > > The protein-ligand complex is constructed using auto dock from the > mol2 > > > > file download from Zinc database. The complex structure then is > > uploaded > > > to > > > > charmm gui and the atom number varies with the mol2 file and pdb > file. > > I > > > > find no way to change the atom order or numbering. > > > > > > > > > > > > > Why this is a problem? Whatever the numbering you get in the output, > you > > > can always renumber the atoms using editconf. Check gmx editconf -h. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > *Regards,* > > *Rahul * > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.