[gmx-users] Protein segment
David
spoel at xray.bmc.uu.se
Thu Sep 11 21:59:00 CEST 2003
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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--
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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