Re: [gmx-users] Simulation of Carbon nanotube
On 6/22/17 8:31 AM, Nikhil Maroli wrote: Thanks, I have given the image of the system in the below link. I thought if I can get Topology and Parameters for CNT alone would be better to go with Charmm-gui. Since I can treat CNT as ligand and upload the parameters will work with the server so in this aspects any suggestion? like how to get those parameters for CNT? Sorry, it is somewhat out of GROMACS question. https://drive.google.com/file/d/0BxaQk_pcR9vicWdDdWV1T0YwTUE/view?usp=sharing I understand what you're doing, I'm just not sure it's worth the effort to try to convert topology and parameter information to CHARMM format (especially if you're not familiar with it) for a periodic molecule (which I honestly don't know if CHARMM will handle correctly). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] Simulation of Carbon nanotube
Thanks, I have given the image of the system in the below link. I thought if I can get Topology and Parameters for CNT alone would be better to go with Charmm-gui. Since I can treat CNT as ligand and upload the parameters will work with the server so in this aspects any suggestion? like how to get those parameters for CNT? Sorry, it is somewhat out of GROMACS question. https://drive.google.com/file/d/0BxaQk_pcR9vicWdDdWV1T0YwTUE/view?usp=sharing Thanks in advance. -- 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.
Re: [gmx-users] Simulation of Carbon nanotube
On 6/22/17 6:59 AM, Nikhil Maroli wrote: Dear Justin, I have generated topology for CNT using gmx x2top. There is cyclic peptide nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to put the whole system into the lipid bilayer. I was using charmm-gui for the input generator since it provides easy hand on CPN, So is it possible to convert the CNT topology which generated with gmx x2top to 'Topology and Parameters' for charmm-gui (*.rtf and *.prm)? Possibly, but I've never tried it. Assuming it's an "infinite" molecule, the periodic bonding could be tricky. You may just want to build the membrane and then write a little script to carve out a cylinder of suitable size later, and overlay your existing coordinates. Probably a lot less effort, in the end. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] Simulation of Carbon nanotube
Dear Justin, I have generated topology for CNT using gmx x2top. There is cyclic peptide nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to put the whole system into the lipid bilayer. I was using charmm-gui for the input generator since it provides easy hand on CPN, So is it possible to convert the CNT topology which generated with gmx x2top to 'Topology and Parameters' for charmm-gui (*.rtf and *.prm)? Thanks in advance. -- 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.
Re: [gmx-users] Simulation of Carbon nanotube
On 6/14/17 12:28 PM, Nikhil Maroli wrote: Dear All, I wanted to simulate a system with Cyclic peptide nanotube and Carbon Nanotubes. Earlier, I used charmm36 for CPN simulations in water and lipids, how can I simulate a system with both CPN and CNT? Charmm36 or is there any other ff and server for the parameters. A CNT topology is simple - all the C atoms are the same aromatic type and they're uncharged unless the CNT is functionalized in some way. gmx x2top can build the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] Simulation of Carbon nanotube
Dear All, I wanted to simulate a system with Cyclic peptide nanotube and Carbon Nanotubes. Earlier, I used charmm36 for CPN simulations in water and lipids, how can I simulate a system with both CPN and CNT? Charmm36 or is there any other ff and server for the parameters. Thanks -- Regards, Nikhil Maroli -- 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.
