[gmx-users] Parametrisation of the heteroatomic pdb

[Justin A. Lemkul]

James Starlight wrote:
> Justin, hello!
> 
> 
> I've found that D and L-isomers must be topological identicaly so I've 
> used topology of Leu and Val residues for Dle and Dva resp.
> 
> I've added information about topology of that two residues to the .rtp  
> .hdb of my force field as well as to the 
> <http://www.gromacs.org/Documentation/File_Formats/.rtp_File>residuetypes.dat 
> <http://www.gromacs.org/Documentation/File_Formats/residuetypes.dat>
> 
> Then I've succsesfull generated topology for gramicidin via pdb2gmx.
> 
> I have only questions about two terminal CAP groups used in the Gramicidin
> 
> It was FOR group on the C-end
> 
> HETATM    1  C   FOR A   1A     -3.690  -1.575  -2.801  1.00  
> 0.00           C 
> HETATM    2  O   FOR A   1A     -3.774  -1.363  -1.586  1.00  
> 0.00           O 
> HETATM    3  H   FOR A   1A     -4.305  -1.047  -3.545  1.00  
> 0.00           H 
> 
> and the ETA group  on the N-end
> 
> HETATM  267  C1  ETA A  15A      5.148  -0.421   8.762  1.00  
> 0.00           C 
> HETATM  268  C2  ETA A  15A      3.657  -0.080   8.832  1.00  
> 0.00           C 
> HETATM  269  N   ETA A  15A      2.813  -1.244   8.933  1.00  
> 0.00           N 
> HETATM  270  O   ETA A  15A      5.921   0.752   8.985  1.00  
> 0.00           O 
> HETATM  271 1HN  ETA A  15A      2.507  -1.491   9.845  1.00  
> 0.00           H 
> HETATM  272  HO  ETA A  15A      5.736   1.339   8.244  1.00  
> 0.00           H 
> HETATM  273 1H1  ETA A  15A      5.410  -1.174   9.531  1.00  
> 0.00           H 
> HETATM  274 2H1  ETA A  15A      5.374  -0.849   7.759  1.00  
> 0.00           H 
> HETATM  275 1H2  ETA A  15A      3.383   0.525   7.938  1.00  
> 0.00           H 
> HETATM  276 2H2  ETA A  15A      3.492   0.565   9.718  1.00  0.00
> 
> I could not find good analogue for that groups in Amber force field so 
> I've desided to deleate that groups temporary.
> Could you tell me how I can add possible Caps on the C and N terms of 
> each chain of my molecule via pdb2gmx ?
> In one tutorial I've found the -term function for that but in my case 
> system didnt suggest me to add new caps
> 

You have to build capping groups onto the termini.  See, for instance the [ACE] 
and [NME] groups in the .rtp file.

-Justin

> 
> 
> James
> 
> 2011/10/28 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     James Starlight wrote:
> 
>         Dear Gromacs users!
> 
>         I've forced with some problem of preparing topology of my input
>         pdb via pdb2gmx.
> 
>         My input structure( gramicidin ion chanell) consist of some
>         heteroatoms due to the presence of the non standart aminoacids
>         in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L
>         analogs)
> 
> 
>         I've tried to parametriesed that structure via different force
>         fields but in all cases there are not suitable topologies for
>         that aminoacids
> 
>         e.g
>         Fatal error:
>         Residue 'FOR' not found in residue topology database
> 
>         How I can solve that problem? I've tried to look for the
>         suitable itp file but could not find it too :(
> 
> 
>     For new protein residues, you do not need an .itp file, you need a
>     suitable .rtp entry such that pdb2gmx can incorporate it into your
>     topology.
> 
>     http://www.gromacs.org/__Documentation/How-tos/__Parameterization
>     <http://www.gromacs.org/Documentation/How-tos/Parameterization>
>     http://www.gromacs.org/__Documentation/How-tos/Adding___a_Residue_to_a_Force_Field
>     <http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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-- 
========================================

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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