<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Do you intend to protonate a pair of cysteins and not make a SS bond? <br >Then pdb2gmx -ss should do the job. <br ><br >Sharada<br ><br ><font size="2" face="Arial"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><br ><strong><em>-- Original Message --</em></strong><br >From: sharada <sharada@ccmb.res.in><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST)<br >Subject: Re: Re: [gmx-users] How to break a disulfide bond ???<br ><br ><meta http-equiv="Content-Type" content="text/html; charset=x-user-defined" >If you donot make it, it is as good as breaking it...<br ><br >Sharada<br ><font size="2" face="Arial"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><br ><strong><em>-- Original Message --</em></strong><br >From: Venkat Reddy <venkat4bt@gmail.com><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Fri, 6 Mar 2009 11:31:57 +0530<br >Subject: Re: [gmx-users] How to break a disulfide bond ???<br ><br >Hai !<br ><br >with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break a particular ss bond (not all).<br >Thank you<br ><br ><br ><DIV CLASS="gmail_quote">On Fri, Mar 6, 2009 at 11:01 AM, sharada <SPAN DIR="ltr"><<A TARGET="_blank" HREF="mailto:sharada@ccmb.res.in">sharada@ccmb.res.in</A>></SPAN> wrote:<br ><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"><DIV><br >pdb2gmx -h<br ><br >sharada<br ><br ><font size="2" face="Arial"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><DIV><DIV> </DIV><DIV CLASS="h5"><br ><strong><em>-- Original Message --</em></strong><br >From: Venkat Reddy <<A TARGET="_blank" HREF="mailto:venkat4bt@gmail.com">venkat4bt@gmail.com</A>><br >To: Discussion list for GROMACS users <<A TARGET="_blank" HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><br >Date: Fri, 6 Mar 2009 10:50:24 +0530<br >Subject: [gmx-users] How to break a disulfide bond ???<br ><br >Hai Every one ! Is it possible to break a disulfide bridge using gromacs ?????If so,Can anybody suggest me, how to do it???<br clear="all" ><br >Thanks for ur valuable time<br ><br >With best wishes<br >Venkat Reddy Chirasani<br >M.Tech Bioinformatics<br >UNIVERSITY OF HYDERABAD<br ></DIV></DIV>_______________________________________________<br >gmx-users mailing list <A TARGET="_blank" HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><br ><A TARGET="_blank" HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><br >Please search the archive at <A TARGET="_blank" HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to <A TARGET="_blank" HREF="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<br >Can't post? Read <A TARGET="_blank" HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></TD></TR></tbody></TABLE></font></DIV><br >_______________________________________________<br >gmx-users mailing list <A TARGET="_blank" HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><br ><A TARGET="_blank" HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><br >Please search the archive at <A TARGET="_blank" HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<br >Please don't post (un)subscribe requests to the list. Use the<br >www interface or send it to <A TARGET="_blank" HREF="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<br >Can't post? Read <A TARGET="_blank" HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><br ></blockquote></DIV><br ><br clear="all" ><br >-- <br >Venkat Reddy Chirasani<br >M.Tech Bioinformatics<br >UNIVERSITY OF HYDERABAD<br >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to gmx-users-request@gromacs.org.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php</TD></TR></tbody></TABLE></font>_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to gmx-users-request@gromacs.org.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php</TD></TR></tbody></TABLE></font></BODY></HTML>