[gmx-users] Protein segment

[David]

On Thu, 2003-09-11 at 21:50, Osmany Guirola Cruz wrote:
>  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
> 
> 
using either position restraint on selected atoms, or using a freeze
group.
> 
> 
> -----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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> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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