<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">This probably is my ignorance but the error and the "bug" goes when I replaced CBX with NAC everywhere.</span><br>
<br><div class="gmail_quote">On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I checked again and the error does not go. Please read the steps below.<br>
<br>
The pdb file I started off with did not have any hydrogens. However, the way I had specified the capping residues in the .rtp file (SEE MARK'S MAIL), I had to specify hydrogens in the pdb file for the capping residues. So I used pymol to add hydrogens to my pdb file. I then used this file with charmm force field. However, pymol had added hydrogens everywhere and this was different from the definition of the standard residues defined in the .rtp file. I could not directly use -ignh because I needed the hydrogens for the capping residues. So I created a file that contained the hydrogens on the capping residues only. This resolved the error related to hydrogens.<br>
<br>
</blockquote>
<br></div>
Probably an easier and more reliable approach would simply be to create an .hdb entry for your capping groups.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Error-from previous mail-NOT RESOLVED<br>
(Fatal error:<br>
There is a dangling bond at at least one of the terminal ends.<br>
Select a proper terminal entry.<br>
For more information and tips for troubleshooting, please check the<br>
GROMACS<br>
I have used Mark's definitions for capping residues in the rtp file.<br>
<br>
In the pdb file, this is what the capping residues look like:<br>
<br>
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60 FR1<br>
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80 FR1<br>
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17 FR1<br>
<br>
</blockquote>
<br></div>
Maybe this is just showing up incorrectly in my mail client, but I wonder if that CH3 is somehow misaligned and therefore not correctly identified. I presume that you changed the residue name in the .rtp file accordingly? I suppose the error message would be different (something like "residue not found") but I just want to make sure. Mark's entry used NAC.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17 FR1<br>
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10 FR1<br>
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60 FR1 )<br>
<br>
The error stated in the previous mail(quoted above) occurred when I chose "none" for the both terminals or the carboxylic terminal option (using -ter). It worked fine if I chose "none" at the N terminal and any other option except "none" at the carboxylic acid terminal. So I chose "none" at N terminal and some option randomly at the carboxylic acid terminal. As expected, it adds a terminal at that end of the residue before my capping residue which is something I DONT want. I <br>
</blockquote>
<br></div>
So does pdb2gmx somehow add the C-terminal cap after the carboxylate terminus?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
havent been able to find a way around it. Interestingly, when I generate a pdb file using -q, and open that pdb file in pymol, I dont get the terminal carboxylic acid that pdb2gmx gives in the .gro file. <br>
</blockquote>
<br></div>
So the cap is applied properly in that structure?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am not sure how to correct this. One way would be to remove those entries from the final .gro and .top file but not sure if that would be right.<br>
<br>
</blockquote>
<br></div>
This all sounds very fishy. This may be worth a bugzilla entry, but only if you can build the structure in a very sound way, probably using .hdb entries (or an appropriate all-atom structure, which you've yet to demonstrate).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Pooja<div class="im"><br>
<br>
<br>
<br>
<br>
<br>
<br>
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul <<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>>> wrote:<br>
<br>
<br>
<br>
Sai Pooja wrote:<br>
<br></div><div class="im">
Follow-up. It is easy to make it work. Just needed to be more<br>
rigorous. Thank you.<br>
<br>
<br>
It would be helpful if you describe what you mean. This error<br>
message is new to me, and appears to reflect new mechanics in the<br>
upcoming Gromacs release. If you describe what the problem was, how<br>
you resolved it, what your pdb2gmx command line was, and anything<br>
else that might be useful, that would likely help others solve this<br>
issue in the future.<br>
<br>
-Justin<br>
<br>
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a><br></div>
<mailto:<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><div><div></div><div class="h5"><br>
<mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>>>> wrote:<br>
<br>
I used -ter option and selected "none" for both terminal ends<br>
but I<br>
still get this error:<br>
<br>
Fatal error:<br>
There is a dangling bond at at least one of the terminal ends.<br>
Select a proper terminal entry.<br>
For more information and tips for troubleshooting, please<br>
check the<br>
GROMACS<br>
I have used Mark's definitions for capping residues in the<br>
rtp file.<br>
<br>
In the pdb file, this is what the capping residues look like:<br>
<br>
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00<br>
1.60 FR1<br>
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00<br>
0.80 FR1<br>
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00<br>
2.17 FR1<br>
<br>
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00<br>
2.17 FR1<br>
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00<br>
2.10 FR1<br>
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00<br>
1.60 FR1<br>
<br>
<br>
<br>
<br>
<br>
<br>
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul<br>
<<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>><br></div></div><div><div></div><div class="h5">
<mailto:<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>>>> wrote:<br>
<br>
<br>
<br>
Sai Pooja wrote:<br>
<br>
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<br>
combining tdb<br>
and rtp<br>
For more information and tips for troubleshooting, please<br>
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>
<br>
<br>
What are you choosing as your termini when running<br>
pdb2gmx? It<br>
should be "none," since by capping, you are not choosing a<br>
protonation state for the N- and C-termini.<br>
<br>
-Justin<br>
<br>
<br>
Pooja<br>
<br>
<br>
<br>
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham<br>
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<mailto:<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><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>><br>
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<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<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>
From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a><br>
<mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br>
<mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a><br></div></div><div class="im">
<mailto:<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>
<mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br></div><div class="im">
<mailto:<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>
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>><br>
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Discussion list for<br>
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<mailto:<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><div><div></div><div class="h5">
<br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br>
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<br>
> I am sorry if I did not frame the question<br>
correctly,<br>
but putting<br>
it very simply, is there a way to use capping residues<br>
with the<br>
charmm forcefield if the residues are --COCH3 and<br>
NHCH3?<br>
<br>
Yes - you edit a copy of the .rtp file in your working<br>
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>
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