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

[maria goranovic]

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 ?


     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>wrote:

>
>
> On 01/20/11, *maria goranovic * <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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110120/70039ff1/attachment.html>