<div>Thankl you.</div>
<div>Well... Indeed, just removed them manually and everything is ok.</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Mon, Apr 16, 2012 at 2:38 PM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Sounds like a bad VMD selection that didn't remove MNZ1 when you did the<br>conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ<br>
in protonated LYS.<br>
<div>
<div class="h5"><br>On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote:<br>> Dear Gmx Users,<br>><br>> I run implicit simulation for 1 us with virtual sites on hydrogens, then<br>> using VMD extracted coordinates into the pdb file. As I want to run<br>
> explicit solvent simulation now I removed hydrogens so that pdb2gmx will<br>> add them. Then I got an error while trying to pdb2gmx using Charmm27:<br>><br>> Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms<br>
> while sorting atoms.<br>><br>> How come this atom appears in my pdb file? Any suggestions?<br>><br>> Thank you,<br>><br>> Steven<br><br></div></div>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<span class="HOEnZb"><font color="#888888"><br><br>--<br>==================================================================<br>Peter C. Lai | University of Alabama-Birmingham<br>Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br><a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br><a href="tel:%28205%29%20690-0808" value="+12056900808">(205) 690-0808</a> |<br>
==================================================================<br><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br>