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]>> 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]>> 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]>>> wrote:
----- Original Message -----
From: Sai Pooja <[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]>>,
Discussion list for
GROMACS users <[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 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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--
Quaerendo Invenietis-Seek and you shall discover.
--
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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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