Sai Pooja wrote:
I checked again and the error does not go. Please read the steps below.
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.
Probably an easier and more reliable approach would simply be to create an .hdb
entry for your capping groups.
Error-from previous mail-NOT RESOLVED
(Fatal error:
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
I have used Mark's definitions for capping residues in the rtp file.
In the pdb file, this is what the capping residues look like:
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60
FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80
FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17
FR1
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.
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17
FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10
FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60
FR1 )
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
So does pdb2gmx somehow add the C-terminal cap after the carboxylate terminus?
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.
So the cap is applied properly in that structure?
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.
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).
-Justin
Pooja
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Sai Pooja wrote:
Follow-up. It is easy to make it work. Just needed to be more
rigorous. Thank you.
It would be helpful if you describe what you mean. This error
message is new to me, and appears to reflect new mechanics in the
upcoming Gromacs release. If you describe what the problem was, how
you resolved it, what your pdb2gmx command line was, and anything
else that might be useful, that would likely help others solve this
issue in the future.
-Justin
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> wrote:
I used -ter option and selected "none" for both terminal ends
but I
still get this error:
Fatal error:
There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.
For more information and tips for troubleshooting, please
check the
GROMACS
I have used Mark's definitions for capping residues in the
rtp file.
In the pdb file, this is what the capping residues look like:
ATOM 33 N CBX 5 8.609 2.722 18.430 1.00
1.60 FR1
ATOM 34 H CBX 5 9.198 3.338 17.946 1.00
0.80 FR1
ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00
2.17 FR1
ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00
2.17 FR1
ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00
2.10 FR1
ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00
1.60 FR1
On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Sai Pooja wrote:
Thanks Marks. I tried it but this is what I get:
Fatal error:
atom N not found in buiding block 1ACE while
combining tdb
and rtp
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Do I need to edit the aminoacids.n.tdb file as well?
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.
-Justin
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
<[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>> wrote:
----- Original Message -----
From: Sai Pooja <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> <mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>,
Discussion list for
GROMACS users <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> <mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>>
> I am sorry if I did not frame the question
correctly,
but putting
it very simply, is there a way to use capping residues
with the
charmm forcefield if the residues are --COCH3 and
NHCH3?
Yes - you edit a copy of the .rtp file in your working
directory and
add whatever you want. Here's what I use in CHARMM
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 0
HH32 HA 0.090 0
HH33 HA 0.090 0
C C 0.510 1
O O -0.510 1
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ NAC ]
[ atoms ]
N NH1 -0.470 1
HN H 0.310 1
CH3 CT3 -0.110 1
HH31 HA 0.090 1
HH32 HA 0.090 1
HH33 HA 0.090 1
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
Mark
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-- Quaerendo Invenietis-Seek and you
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
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-- Quaerendo Invenietis-Seek and you shall discover.
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Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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