<pre>Thaks for your suggesion... <br> <br>I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the <br>problem I encounter is that the pdb2gmx produces the topologies where hydrogens <br>sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly <br>since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I <br>mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. <br>So my questions are;<br><br>1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care <br>of hydrogens sitting on carbon atoms in a sugar molecule explicitly?<br><br>2- How can I most reliably produce topologies for my disaccharide that will <br>be placed in a water box to perform MD?<br><br><br>I am quite new to MD methods therefore I apologize already now if I put <br>forward something incoherent.<br><br>Thanks for the help,</pre> <br><br><b><i>Tsjerk
Wassenaar <tsjerkw@gmail.com></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Parichita,<br><br>My guess is you only thought to have 1-6 linkage, because the atoms<br>seemed so nicely involved in the .pdb file. But you'll have to define<br>a bond explicitly or it won't be there to break in the first place. I<br>think you need to read up on topologies, force fields and general<br>background about simulating molecular systems. Chapter 5 is a must. If<br>you continue on this path, note that sugar dihedrals, especially the<br>ones connecting the rings, are complex. Check out Roberto Lins' paper<br>on the 45a3 force field.<br><br>Tsjerk<br><br>On 9/17/07, Mark Abraham <Mark.Abraham @anu.edu.au=""> wrote:<br>> parichita parichita wrote:<br>> > Hi again.....<br>> > Thank you for your help....<br>> > I found my MANA in the ffG53a5.rtp and i can prepare<br>> > the
.gro and .top file from pdb2gmx.<br>> > Now , i am facing another problem after solvation of<br>> > my solute when i run the minimization the 1-6 linkage<br>> > was broken ......<br>> > please help me out ........<br>><br>> "linkage was broken" doesn't help us help you. Please describe in detail<br>> what you observed and why you think it was wrong.<br>><br>> Mark<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<br>><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet
Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<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<br></Mark.Abraham></blockquote><br><BR><BR><DIV>
<DIV><FONT face=arial color=#0000bf>Parichita Mazumder <BR>Junior Research Fellow <BR>C/O Dr. Chaitali Mukhopadhayay <BR>Department of Chemistry <BR>University of Calcutta <BR>92,A P C Road <BR>Kolkata-700009 <BR>India.</FONT></DIV></DIV><p> 
<!--3--><hr size=1></hr> Save all your chat conversations. <a href="http://in.rd.yahoo.com/tagline_webmessenger_3/*http://in.messenger.yahoo.com/webmessengerpromo.php">Find them online.</a>