[gmx-users] Protein segment

[Osmany Guirola Cruz]

 How can I do(If it's posible) a simulation of a protein in water whith
a segment(for example residue 20-50) that not move, and the others free
of movment




-----Original Message-----
From: Marc Ceruso [mailto:mceruso at physbio.mssm.edu] 
Sent: Thursday, September 11, 2003 2:26 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] building block-rtp


Hi-

Which force field are you using (ffgmx) ?
Did you change the name of this residue to XXX in the pdb file? Do you
get an error from pdb2gmx? marc


On Thu, 11 Sep 2003, Lakshmi Padmavathi wrote:

> Dear gromacs users,
>
> i would like make one building block for a abnormal residue (not usual

> amino acid but has aminoacid properties).
>
> so,
> i creatred one building block. i inserted in ffgmx.rtp, ffgmx.hdb and 
> in aminoacids.dat.
>
> but it couldnot recognise the file in rtp database when i run pdb2gmx.
>
> i request you all to give suggestion for this.
>
> i will be very thankful to you.
>
> i paste my building block here.
>
> [ XXX ]
>  [ atoms ]
>      N     N  -0.280     0
>      H     H   0.280     0
>     CA   CH1   0.000     1
>     CB   CH2   0.000     2
>     S1     S   0.000     3
>      S     S   0.000     4
>     C9   CH2   0.000	 5
>     C8   CH3   0.000     6
>     C7   CH3   0.000     7
>     C6   CH3   0.000     8
>     C5   CH3   0.000     9
>     C4    CB   0.110    10
>     N1  NR5*   0.080    10
>     OH     O  -0.300    10
>     C1    CB   0.110    10
>     C2    CB   0.000    11
>     C3   CR5   0.000    12
>      C     C   0.380     4
>      O     O  -0.380     4
>  [ bonds ]
>      N     H
>      N    CA
>     CA     C
>      C     O
>     -C     N
>     CA    CB
>     CB    S1
>     S1     S
>      S    C9
>     C9    C2
>     C2    C3
>     C3    C4
>     C6    C4
>     C5    C4
>     C4    N1
>     OH    N1
>     C2    C1
>     N1    C1
>     C8    C1
>     C1    C7
>  [ impropers ]
>      N    -C    CA     H
>     -C   -CA     N    -O
>     CA     N     C    CB
>     N1    C1    OH    C4
>     C2    C1    C3    C9
>     C1    C7    C8    N1
>     C4    N1    C5    C6
>
>
>
>
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