Follow-up. <div>It is easy to make it work. Just needed to be more rigorous. Thank you.<div><br><div class="gmail_quote">On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>I used -ter option and selected "none" for both terminal ends but I still get this error:</div><div><br>
</div><div>Fatal error:</div><div>There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.</div><div class="im">
<div>For more information and tips for troubleshooting, please check the GROMACS</div></div><div> I have used Mark's definitions for capping residues in the rtp file.</div><div><br></div><div>In the pdb file, this is what the capping residues look like:</div>
<div><br></div><div><div>ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60 FR1</div><div>ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80 FR1</div><div>ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17 FR1</div>
</div><div><br></div><div><div>ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17 FR1</div><div>ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10 FR1</div><div>ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60 FR1</div>
</div><div><div></div><div class="h5"><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><br><div class="gmail_quote">On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks Marks. I tried it but this is what I get:<br>
<br>
Fatal error:<br>
atom N not found in buiding block 1ACE while combining tdb and rtp<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
Do I need to edit the aminoacids.n.tdb file as well?<br>
</blockquote>
<br></div>
What are you choosing as your termini when running pdb2gmx? It should be "none," since by capping, you are not choosing a protonation state for the N- and C-termini.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Pooja<div><br>
<br>
<br>
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
<br>
----- Original Message -----<br></div><div>
From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>>><br>
Date: Friday, July 2, 2010 7:28<br>
Subject: Re: [gmx-users] Capping residues<br></div><div><div></div><div>
To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>, Discussion list for<br>
GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
> I am sorry if I did not frame the question correctly, but putting<br>
it very simply, is there a way to use capping residues with the<br>
charmm forcefield if the residues are --COCH3 and NHCH3?<br>
<br>
Yes - you edit a copy of the .rtp file in your working directory and<br>
add whatever you want. Here's what I use in CHARMM<br>
<br>
[ ACE ]<br>
[ atoms ]<br>
CH3 CT3 -0.270 0<br>
HH31 HA 0.090 0<br>
HH32 HA 0.090 0<br>
HH33 HA 0.090 0<br>
C C 0.510 1<br>
O O -0.510 1<br>
[ bonds ]<br>
C CH3<br>
C +N<br>
CH3 HH31<br>
CH3 HH32<br>
CH3 HH33<br>
O C<br>
[ impropers ]<br>
C CH3 +N O<br>
<br>
[ NAC ]<br>
[ atoms ]<br>
N NH1 -0.470 1<br>
HN H 0.310 1<br>
CH3 CT3 -0.110 1<br>
HH31 HA 0.090 1<br>
HH32 HA 0.090 1<br>
HH33 HA 0.090 1<br>
[ bonds ]<br>
-C N<br>
N HN<br>
N CH3<br>
CH3 HH31<br>
CH3 HH32<br>
CH3 HH33<br>
<br>
[ impropers ]<br>
N -C CH3 HN<br>
-C CH3 N -O<br>
<br>
Mark<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div><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/search" target="_blank">http://www.gromacs.org/search</a> before<br>
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" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</div></blockquote><div>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div></div>