[gmx-users] S-S bond
Hi, I want to functionalize ZnS nanotube with different molecules which all have sulfur in their structures, like cystein amino acid and ... . I want to study the interaction of this functionalized nanotube with different proteins. I use DFT for calculating the partial charges and bond length in ZnS nanotube and made an .itp file for it. If i know that cystein (and all those molecules) can BIND to ZnS with their sulfur atom, can AMBER define this this S(from cystein)-S(from ZnS nanotube) bond? Is this special S-S bond like that S-S which is in amber? There is an article which correspond to interaction of ZnS with cystein by umbrella sampling. In this article the binding energy and bond length in minimum PMF is calculated. How about this bond length? It couldn't be used as S-S bond length for ZnS nanotube cystein? Is it better to use DFTcalculation for all these structures and just do functionalized nanotube with protein by AMBER force field? Could you please help me? Best regards -- 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] s-s bond recognition
Hi everyone I’m going to run -pdb2gmx on my protein with PDB code of 2O6X. This protein has three S-S bonds within its crystal structure, but, after running of -pdb2gmx, only 2 of them recognized as S-S bond. I think that the distance between S atom of Cys253 and its counterpart of Cys302 is too long to form S-S bond. What can I do? Can I force these residues to form S-S bond in .gro file? -- Thanks in Advance Hamid Mahdiuni Dept. of Biology, Faculty of Science Razi University P.O.Box 6714967346 Kermanshah-Iran Tel: +98 831 4274545 Fax: +98 831 4274545 E-mail : mahdi...@ibb.ut.ac.ir mahdi...@gmail.com -- 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] s-s bond recognition
Hello. I would suggest you to first try energy minimization on the protein alone and see whether it solves the issue. If not, then try MD (without any S-S bonds) with distance restraints on the sulfur atoms of the particular Cys residues. See if that resolves the issue. Regards, Abhishek On Sun, Nov 23, 2014 at 6:56 PM, Hamid Mahdiuni mahdi...@gmail.com wrote: Hi everyone I’m going to run -pdb2gmx on my protein with PDB code of 2O6X. This protein has three S-S bonds within its crystal structure, but, after running of -pdb2gmx, only 2 of them recognized as S-S bond. I think that the distance between S atom of Cys253 and its counterpart of Cys302 is too long to form S-S bond. What can I do? Can I force these residues to form S-S bond in .gro file? -- Thanks in Advance Hamid Mahdiuni Dept. of Biology, Faculty of Science Razi University P.O.Box 6714967346 Kermanshah-Iran Tel: +98 831 4274545 Fax: +98 831 4274545 E-mail : mahdi...@ibb.ut.ac.ir mahdi...@gmail.com -- 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.
Re: [gmx-users] s-s bond recognition
Thanks Abhishek, I will do it. Sent from Samsung Mobile div Original message /divdivFrom: Abhi Acharya abhi117acha...@gmail.com /divdivDate:23/11/2014 6:03 PM (GMT+03:30) /divdivTo: Discussion list for GROMACS users gmx-us...@gromacs.org /divdivCc: /divdivSubject: Re: [gmx-users] s-s bond recognition /divdiv /divHello. I would suggest you to first try energy minimization on the protein alone and see whether it solves the issue. If not, then try MD (without any S-S bonds) with distance restraints on the sulfur atoms of the particular Cys residues. See if that resolves the issue. Regards, Abhishek On Sun, Nov 23, 2014 at 6:56 PM, Hamid Mahdiuni mahdi...@gmail.com wrote: Hi everyone I’m going to run -pdb2gmx on my protein with PDB code of 2O6X. This protein has three S-S bonds within its crystal structure, but, after running of -pdb2gmx, only 2 of them recognized as S-S bond. I think that the distance between S atom of Cys253 and its counterpart of Cys302 is too long to form S-S bond. What can I do? Can I force these residues to form S-S bond in .gro file? -- Thanks in Advance Hamid Mahdiuni Dept. of Biology, Faculty of Science Razi University P.O.Box 6714967346 Kermanshah-Iran Tel: +98 831 4274545 Fax: +98 831 4274545 E-mail : mahdi...@ibb.ut.ac.ir mahdi...@gmail.com -- 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. -- 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] s-s bond recognition
On 11/23/14 8:26 AM, Hamid Mahdiuni wrote: Hi everyone I’m going to run -pdb2gmx on my protein with PDB code of 2O6X. This protein has three S-S bonds within its crystal structure, but, after running of -pdb2gmx, only 2 of them recognized as S-S bond. I think that the distance between S atom of Cys253 and its counterpart of Cys302 is too long to form S-S bond. What can I do? Can I force these residues to form S-S bond in .gro file? Make a copy of specbond.dat in the working directory and adjust the reference distance for the disulfide. pdb2gmx should print out the distance matrix, so you know how far the atoms are to make the proper adjustment. http://www.gromacs.org/Documentation/File_Formats/specbond.dat -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.
