Thanks Sharada madam n justin sir for ur kind attention.I followed ur command "pdb2gmx -ss".its asking like
Link CYS-37 SG-306 and CYS-59 SG-453 (y/n) ?n Link CYS-44 SG-358 and CYS-50 SG-390 (y/n) ?y Link CYS-72 SG-560 and CYS-101 SG-764 (y/n) ?y Link CYS-82 SG-628 and CYS-93 SG-707 (y/n) ?y Link CYS-150 SG-1137 and CYS-156 SG-1173 (y/n) ?y Link CYS-203 SG-1546 and CYS-258 SG-1984 (y/n) ?y Link CYS-210 SG-1603 and CYS-231 SG-1767 (y/n) ?y actually i want to break the s-s bond between CYS37 n CYS59 . so i've given the options like as shown above. When i again visualized the pdb in pymol,its showing the disulfides as it is (no break between CYS37 n CYS59). Can u suggest me wat to do ???? Thanks for giving reply. On Fri, Mar 6, 2009 at 7:24 PM, sharada <[email protected]> wrote: > Do you intend to protonate a pair of cysteins and not make a SS bond? > Then pdb2gmx -ss should do the job. > > Sharada > > > *-- Original Message --* > From: sharada <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST) > Subject: Re: Re: [gmx-users] How to break a disulfide bond ??? > > If you donot make it, it is as good as breaking it... > > Sharada > > *-- Original Message --* > From: Venkat Reddy <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Date: Fri, 6 Mar 2009 11:31:57 +0530 > Subject: Re: [gmx-users] How to break a disulfide bond ??? > > Hai ! > > with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break > a particular ss bond (not all). > Thank you > > > On Fri, Mar 6, 2009 at 11:01 AM, sharada <[email protected]> wrote: > >> >> pdb2gmx -h >> >> sharada >> >> >> >> *-- Original Message --* >> From: Venkat Reddy <[email protected]> >> To: Discussion list for GROMACS users <[email protected]> >> Date: Fri, 6 Mar 2009 10:50:24 +0530 >> Subject: [gmx-users] How to break a disulfide bond ??? >> >> Hai Every one ! Is it possible to break a disulfide bridge using gromacs >> ?????If so,Can anybody suggest me, how to do it??? >> >> Thanks for ur valuable time >> >> With best wishes >> Venkat Reddy Chirasani >> M.Tech Bioinformatics >> UNIVERSITY OF HYDERABAD >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Venkat Reddy Chirasani > M.Tech Bioinformatics > UNIVERSITY OF HYDERABAD > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD Laboratory of Computational Biology Centre for DNA Fingerprinting and Diagnostics
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