maria goranovic wrote:
Gee. My mistake then. I did not realize the difference between -COO and
Zwitterion_COO-.
However, when I use the zwitterion termini on both ends of the other
chain, the total charge is 4.010, which is also *slightly*ยด disturbing.
I have seen numbers like 2.999999, which are still better. Is 4.010
acceptable within rounding off errors?
Nothing greater than 0.0001 or so should be considered a rounding problem. With
0.01, you have another problem.
-Justin
thank you for helping
-Maria
On Thu, Jan 20, 2011 at 2:00 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
maria goranovic wrote:
I did use -ter and chose -COO and NH3+. Am i supposed to chose
Zwitterion_COO- and Zwitterion_NH3+ ?
That's what I said, and that's what you have, isn't it? A single
amino acid that should have both its termini charged?
-Justin
On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
maria goranovic wrote:
Hi
I have figured out the vacuum slow problem. It turns out
I was
using PBC in vacuum with PME. It is now fixed.
The other problem is still there. My protein has 2
chains. one
chain is simply a glutamate residue. Its charge (both
terminii
charged is -1.11 instead of -1). here is the section of the
topology with the charges. Why does pdb2gmx assign a
charge of
-1.11 instead of -1 if there is a free glutamate molecule
with
NH3+ and COO- at the terminii ?
You're not choosing the termini correctly. Use -ter with pdb2gmx
and select the zwitterion forms of both termini.
-Justin
1 opls_287 484 GLU N 1 -0.3
14.0067 ; qtot -0.3
2 opls_290 484 GLU H1 1 0.33
1.008 ; qtot 0.03
3 opls_290 484 GLU H2 1 0.33
1.008 ; qtot 0.36
4 opls_290 484 GLU H3 1 0.33
1.008 ; qtot 0.69
5 opls_283 484 GLU CA 1 0.04
12.011 ; qtot 0.73
6 opls_140 484 GLU HA 1 0.06
1.008 ; qtot 0.79
7 opls_136 484 GLU CB 2 -0.12
12.011 ; qtot 0.67
8 opls_140 484 GLU HB1 2 0.06
1.008 ; qtot 0.73
9 opls_140 484 GLU HB2 2 0.06
1.008 ; qtot 0.79
10 opls_274 484 GLU CG 3 -0.22
12.011 ; qtot 0.57
11 opls_140 484 GLU HG1 3 0.06
1.008 ; qtot 0.63
12 opls_140 484 GLU HG2 3 0.06
1.008 ; qtot 0.69
13 opls_271 484 GLU CD 4 0.7
12.011 ; qtot 1.39
14 opls_272 484 GLU OE1 4 -0.8
15.9994 ; qtot 0.59
15 opls_272 484 GLU OE2 4 -0.8
15.9994 ; qtot -0.21
16 opls_271 484 GLU C 5 0.7
12.011 ; qtot 0.49
17 opls_272 484 GLU O1 5 -0.8
15.9994 ; qtot -0.31
18 opls_272 484 GLU O2 5 -0.8
15.9994 ; qtot -1.11
On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>> wrote:
On 01/20/11, *maria goranovic *
<mariagorano...@gmail.com <mailto:mariagorano...@gmail.com>
<mailto:mariagorano...@gmail.com
<mailto:mariagorano...@gmail.com>>
<mailto:mariagorano...@gmail.com
<mailto:mariagorano...@gmail.com>
<mailto:mariagorano...@gmail.com
<mailto:mariagorano...@gmail.com>>>> wrote:
Hi
I have a protein whose topology I built using pdb2gmx
with the -ss
option and the opls-aa force field. When I run grompp,
the total
charge on the protein is reported as 2.9 (not
2.999). Why a
non-zero charge? Does this have something to do
with the
disulfide
bridge?
Something is materially wrong, like mangled termini.
Have a
look at
the resulting structure.
Secondly, when I run a simulation of the same protein
(7000 atoms)
with certain restraints in vacuum, the simulation runs
very slow.
I am wondering why. I am not using particle
decomposition. the box
size is 50 x 50 x 50 nm. Using 4.5.3
Have a look at the end of the .log file for some
performance
data.
How are you assessing "very slow"?
Mark
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-- Maria G.
Technical University of Denmark
Copenhagen
-- ========================================
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> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Maria G.
Technical University of Denmark
Copenhagen
--
========================================
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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--
Maria G.
Technical University of Denmark
Copenhagen
--
========================================
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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