Thanks Sharada madam n justin sir for ur kind attention.I followed ur command "pdb2gmx -ss".its asking like<br><br>Link CYS-37 SG-306 and CYS-59 SG-453 (y/n) ?n<br>Link CYS-44 SG-358 and CYS-50 SG-390 (y/n) ?y<br>
Link CYS-72 SG-560 and CYS-101 SG-764 (y/n) ?y<br>Link CYS-82 SG-628 and CYS-93 SG-707 (y/n) ?y<br>Link CYS-150 SG-1137 and CYS-156 SG-1173 (y/n) ?y<br>Link CYS-203 SG-1546 and CYS-258 SG-1984 (y/n) ?y<br>Link CYS-210 SG-1603 and CYS-231 SG-1767 (y/n) ?y<br>
<br>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 ????<br>
Thanks for giving reply. <br><div class="gmail_quote">On Fri, Mar 6, 2009 at 7:24 PM, sharada <span dir="ltr"><<a href="mailto:sharada@ccmb.res.in">sharada@ccmb.res.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Do you intend to protonate a pair of cysteins and not make a SS bond? <br>Then pdb2gmx -ss should do the job. <br><font color="#888888"><br>Sharada<br><br></font><font face="Arial" size="2"><table style="border-color: blue; border-left: 1px solid blue; padding-left: 5px;">
<tbody><tr><td><div class="im"><br><b><i>-- Original Message --</i></b><br>From: sharada <<a href="mailto:sharada@ccmb.res.in" target="_blank">sharada@ccmb.res.in</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
</div><div><div></div><div class="h5">Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST)<br>Subject: Re: Re: [gmx-users] How to break a disulfide bond ???<br><br>If you donot make it, it is as good as breaking it...<br><br>Sharada<br>
<font face="Arial" size="2"><table style="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><tr><td><br><b><i>-- Original Message --</i></b><br>From: Venkat Reddy <<a href="mailto:venkat4bt@gmail.com" target="_blank">venkat4bt@gmail.com</a>><br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><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 href="mailto:sharada@ccmb.res.in" target="_blank">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 face="Arial" size="2"><table style="border-color: blue; border-left: 1px solid blue; padding-left: 5px;">
<tbody><tr><td><div><div> </div><div><br><b><i>-- Original Message --</i></b><br>From: Venkat Reddy <<a href="mailto:venkat4bt@gmail.com" target="_blank">venkat4bt@gmail.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">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 href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
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M.Tech Bioinformatics<br>UNIVERSITY OF HYDERABAD<br>Laboratory of Computational Biology<br>Centre for DNA Fingerprinting and Diagnostics<br>