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

[maria goranovic]

I did use -ter and chose -COO and NH3+. Am i supposed to chose
Zwitterion_COO- and Zwitterion_NH3+ ?

On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <jalemkul at 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.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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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