[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

[Justin A. Lemkul]

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.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
> 
> 
> 
>     On 01/20/11, *maria goranovic * <mariagoranovic at gmail.com
>     <mailto:mariagoranovic at 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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