[gmx-users] Parametrisation of the heteroatomic pdb

[James Starlight]

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



James

2011/10/28 Justin A. Lemkul <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 | (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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