[gmx-users] How to obtain a proper structure for glycine?

[Dawid das]

Oh, I'm sorry for misleading you. You need use

-ter

The -noter means that you DON'T want to choose protonation yourself.
Give this one a try.

2017-08-06 20:38 GMT+02:00 ZHANG Cheng <272699575 at qq.com>:

> Hi Dawid,
> Thank you. However, I still got three hydrogens after running:
>
>
> gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce -noter
>
>
> gly_processed.gro:
>
>
> Glycine aRginine prOline Methionine Alanine Cystine Serine    10  3936GLY
>     N    1  -0.191  -0.011  -0.008  3936GLY     H1    2  -0.275   0.042
> -0.002  3936GLY     H2    3  -0.186  -0.055  -0.098  3936GLY     H3    4
> -0.190  -0.081   0.063  3936GLY     CA    5  -0.075   0.077   0.010
> 3936GLY    HA1    6  -0.078   0.147  -0.062  3936GLY    HA2    7  -0.083
>  0.121   0.099  3936GLY      C    8   0.056   0.002   0.001  3936GLY
>  O1    9   0.047  -0.127   0.004  3936GLY     O2   10   0.163   0.059
> -0.007    0.43801   0.27464   0.19713
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Mon, Aug 7, 2017 02:20 AM
> To:  "Mark Abraham"<mark.j.abraham at gmail.com>; "gmx-users"<
> gmx-users at gromacs.org>; "gromacs.org_gmx-users"<gromac
> s.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  Re:  [gmx-users] How to obtain a proper structure for glycine?
>
>
>
> Hi Mark,
> Thank you. I have a glycine PDB:
>
>
> ATOM      1  N   GLY  3936      -1.908  -0.113  -0.081  1.00 20.00
> ATOM      2  CA  GLY  3936      -0.753   0.774   0.097  1.00 20.00
> ATOM      3  C   GLY  3936       0.558   0.024   0.014  1.00 20.00
> ATOM      4  O   GLY  3936       0.474  -1.274   0.036  1.00 20.00
> ATOM      5  OXT GLY  3936       1.629   0.589  -0.066  1.00 20.00
> END
>
>
>
> Then, I use:
>
>
> gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce
>
>
> and got gly_processed.gro:
>
>
> Glycine aRginine prOline Methionine Alanine Cystine Serine
>     8
>  3936GLY      N    1  -0.191  -0.011  -0.008
>  3936GLY     H1    2  -0.275   0.042  -0.002
>  3936GLY     H2    3  -0.186  -0.055  -0.098
>  3936GLY     H3    4  -0.190  -0.081   0.063
>  3936GLY     CA    5  -0.075   0.077   0.010
>  3936GLY      C    6   0.056   0.002   0.001
>  3936GLY     O1    7   0.047  -0.127   0.004
>  3936GLY     O2    8   0.163   0.059  -0.007
>    0.43801   0.20480   0.16112
>
>
>
> Can I ask, why there are still 3 hydrogens attached to the nitrogen?
>
>
> Yours sincerely
> Cheng
>
>
> ------------------ Original ------------------
> From:  "Mark Abraham";<mark.j.abraham at gmail.com>;
> Date:  Mon, Aug 7, 2017 01:48 AM
> To:  "gmx-users"<gmx-users at gromacs.org>; "gromacs.org_gmx-users"<gromac
> s.org_gmx-users at maillist.sys.kth.se>;
> Cc:  "ZHANG Cheng"<272699575 at qq.com>;
> Subject:  Re: [gmx-users] How to obtain a proper structure for glycine?
>
>
>
>
> Hi,
>
> Prodrg is not gromacs software, so there is probably a better place to ask
> this question. I'd also look at their docs to find out how to suggest a
> carboxylic acid.
>
> Mark
>
> On Sun, 6 Aug 2017 18:09 ZHANG Cheng <272699575 at qq.com> wrote:
>
> Dear Gromacs,
>  I would like to perform simulations for a protein with glycines.
>
>
>  I think I should use "insert-molecules" as shown on
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/biphasic/01_genconf.html
>
>
>  So I went to PRODRG2 Server to obtain the glycine structure by "text
> drawing":
>
>
>      O
>      "
>  N-C-C-O
>
>
>  But I got a suggested structure of NH3-CH2-COO, instead of NH2-CH2-COOH.
> Can I ask why is that?
>
>
>  Thank you.
>
>
>  Yours sincerely
>  Cheng
>  --
>  Gromacs Users mailing list
>
>  * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>  * For (un)subscribe requests visit
>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>