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

[ZHANG Cheng]

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"<gromacs.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"<gromacs.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
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