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[gmx-users] Insertion of chromium III ion into lipid bilayer
Hi, I want to add chromium III ion into lipid bilayer. I have included cr entry in the ions.itp file, and I used grompp it shows error like Atom types cr+3 is not found. After removing cr ions from the ions.itp file it works and after using genion to add cr3+ ions into lipid the following command was used. genion -s ions.tpr -o dppc_solv_ions.gro -p topol.top -pname CR -pq 3 But it shows ""No ions to add and no potential to calculate.. "" Is it necessary to include chromium entry in the ions.itp file? What file i should modify to add cr into lipid? Please explain me to solve this.. Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Insertion-of-chromium-III-ion-into-lipid-bilayer-tp5011884.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] Insertion of chromium III ion into lipid bilayer
First, can you successfully add an ion that the force field already knows about, like potassium? Second, does the force field know about chromium? If not, who does? Mark On Sat, Oct 19, 2013 at 4:27 PM, Sathya wrote: > Hi, > > I want to add chromium III ion into lipid bilayer. I have included cr > entry in the ions.itp file, and I used grompp it shows error like Atom > types cr+3 is not found. After removing cr ions from the ions.itp file it > works and after using genion to add cr3+ ions into lipid the following > command was used. > > genion -s ions.tpr -o dppc_solv_ions.gro -p topol.top > -pname CR -pq 3 > > But it shows ""No ions to add and no potential to calculate.. "" > Is it necessary to include chromium entry in the ions.itp file? What file > i > should modify to add cr into lipid? > Please explain me to solve this.. > > Thanks > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Insertion-of-chromium-III-ion-into-lipid-bilayer-tp5011884.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] Insertion of chromium III ion into lipid bilayer
On 10/19/13 10:27 AM, Sathya wrote: Hi, I want to add chromium III ion into lipid bilayer. I have included cr entry in the ions.itp file, and I used grompp it shows error like Atom types cr+3 is not found. After removing cr ions from the ions.itp file it works and after using genion to add cr3+ ions into lipid the following command was used. genion -s ions.tpr -o dppc_solv_ions.gro -p topol.top -pname CR -pq 3 But it shows ""No ions to add and no potential to calculate.. "" Is it necessary to include chromium entry in the ions.itp file? What file i should modify to add cr into lipid? Please explain me to solve this.. Entries in ions.itp are dependent upon those atom types actually existing in the force field. If the Cr(III) ion has not been parametrized for your force field (which is unlikely to be true for any of the force fields in Gromacs), then there's not much you can do besides derive the parameters yourself. I seriously doubt that any additive biomolecular force field will adequately represent a transition metal like Cr. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] Re: Insertion of chromium III ion into lipid bilayer
Dear Justin, Please Tell me is there any possible option for inserting cr into into DPPC bilayer. -- View this message in context: http://gromacs.5086.x6.nabble.com/Insertion-of-chromium-III-ion-into-lipid-bilayer-tp5011884p5011886.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Insertion of chromium III ion into lipid bilayer
On 10/19/13 11:53 AM, Sathya wrote: Dear Justin, Please Tell me is there any possible option for inserting cr into into DPPC bilayer. Well, anything is possible. You'd have to define an atomtype that represents Cr, which will involve deriving suitable LJ parameters that reproduce some experimental observable that is in some way compatible with the underlying theory of the lipid force field. Then you can incorporate that information into ffnonbonded.itp and ions.itp and proceed. As for whether or not any of that will yield a sensible simulation, I would be highly skeptical. Additive MM force fields are not particularly adept at dealing with highly charged ions, and transition elements are particularly challenging because there are elements of the physics that you simply can't hope to get right with "standard" biomolecular force fields. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
