Hi, Sangeun Thank you so much for your detailed instruction. I can mutate PRO to HYP now. Regards,
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of sangeunjee Sent: Friday, 1 May 2015 9:36 AM To: gmx-us...@gromacs.org Subject: [gmx-users] 회신: Re: Generating topology file containing HYP Dear Ming Tang I am also using free version. To concert proline to hydroxypropine, 1. Read your pdb file using discovery studio visualizer 2. You will find there is list of menu in the left side of the screen. There is an option to draw specific amino acids. Here you can choose mutate to change proline to other one. I hope it helps, Sangeun Jee <div>-------- 원본 메시지 --------</div><div>발신: Ming Tang <m21.t...@qut.edu.au> </div><div>날짜:30/04/2015 02:09 (GMT-05:00) </div><div>수신: gmx-us...@gromacs.org </div><div>제목: Re: [gmx-users] Generating topology file containing HYP </div><div> </div>Dear, sangeun Thanks for your help. I have downloaded and installed Discovery Studio Visualizer, and found only limited amount of its ability is available for free. Do you think I can convert proline into hydroxyproline using its free function? Detail guidance will be appreciate. Thanks in advance, Best regards. -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of sang eun jee Sent: Thursday, 30 April 2015 1:01 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Generating topology file containing HYP Dear Ming Tang As long as I know, Discovery studio visualizer can do the mutation from proline to hydroxyproline in a simple way. Hope it helps, Sangeun Jee On Wed, Apr 29, 2015 at 5:42 AM, Ming Tang <m21.t...@qut.edu.au> wrote: > Dear all, > > I have a pdb file, and need to convert some of the proline to > hydroxyproline. Can I use pdb2gmx to convert proline to hydroxyproline > when generating the topology file? If I cannot, then which kind of > software can be used to convert proline to hydroxyproline when > generating the topology file? > > Thanks in advance, > Regards, > Ming > -- > 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. > -- Post Doctoral Researcher School of Materials Science and Engineering Georgia Institute of Technology -- 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. -- 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.
