Hi Yegor,<br><br>To start with, please refrain from sending mails to persons in stead of to the mailing list, in particular when the person is also on the mailing list (now I got this message twice!). On the mailing list there is a higher probability of getting a sensible answer, since there are more people reading that than there are reading my mailbox (I hope).
<br><br>It is not enough to only define a bond. where two atoms are bonded in a larger construct, there are also angles, dihedrals and possibly improper dihedrals. Furthermore, the atoms on either side of the bond should not 'see' each other in any other way than through the bonded terms. They have to be excluded. It can be that your sulfur atom has a non-bonded interaction with a nearby atom, which it shouldn't have, giving rise to a large force.
<br><br>Best regards,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 2/19/06, <b class="gmail_sendername">X.Periole</b> <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Sun, 19 Feb 2006 09:22:41 -0800 (PST)<br> Yegor Isakov <<a href="mailto:gromacs_problems@yahoo.com">gromacs_problems@yahoo.com</a>> wrote:<br>> I appreciate if anybody could answer my question?<br>> ,<br>
> My molecules continue blowing out. I have got a<br>>peptide where a carbonyl group is connected to cysteine<br>>through S atom (-S-CO-). I inserted my topology (the<br>>whole set including peptide.top
, peptide.gro, and<br>>posre.itp ) into gmxdemo script (water) and run it the<br>>same way as the demo cpeptide. My molecule blows out at<br>>the third step of the run. In the program output I have<br>>got a message that the force is concentrated on the S
<br>>atom.<br>> I have got another molecule where carbonyl group<br>>was attached to protein through NH group (-NH-CO-). This<br>>bond is stable enough and the molecule runs fine up to<br>>3000 steps.
<br>> Thus, I concluded that the problem is that (-S-CO-)<br>>bond. Actually I did not find this bond in the libraries<br>>and I introduced it myself into my topology by just<br>>adding the the physical length of the bond. I believe
<br>>that's not enough.<br>> My question is: what I need to do to introduce into<br>>my MD model a new bond that was not previously described<br>>in those libraries? The manual does not cover this topic<br>
>explicitly.<br>><br>it is called distance restraints, 4.2.14 in manual gmx3.2.<br><br>XAvier<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a 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><br>Tsjerk A. Wassenaar,
M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>