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 <[email protected]
<mailto:[email protected]>> wrote:
On 01/20/11, *maria goranovic * <[email protected]
<mailto:[email protected]>> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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