Dear Axel and Lammps-users,
I followed the discussion on the following thread in order to generate a coordinate date file for Lammps. This is my first experience at using a pdb file for MD data-input. As pointed out, I was able to generate the lammps data file without any of the bond angles and dihedrals. Also, values for xlo xhi etc. came 0.0, possibly because further details were not given in the VMD console interface.
I am in the process of setting up an equilibrium MD simulation for CaCl2.6H20 and the pdb file obtained from the net is attached. I was trying to look in the VMD manuals for discussion on topotools so that a complete lammps data file could be generated, but it seems that VMD beta manual is not published, and the older versions lack this feature. Any description or directions on how to build the complete lammps data from a pdb using vmd would be very useful.
Also, this pdb file seems to be missing the hydrogen atoms present in the salt hydrate. Is this normal, and if yes then how should the H atoms be included in data file ?
Thank you.
Ganesh
— On Fri, 19/6/09, Axel Kohlmeyer [email protected] wrote:
> From: Axel Kohlmeyer [email protected]
> Subject: Re: [lammps-users] help regarding converting from pdb to lammps data file
> To: “vishnu gopalakrishnan” <vishnu.gopalmech@…24…>
> Cc: [email protected]
> Date: Friday, 19 June, 2009, 6:46 PM
>
> On Fri, 2009-06-19 at 16:30 +0530, vishnu gopalakrishnan wrote:
>
> dear vishnu,
>
> > dear lammps users,
> >
> > suppose the bonds in pdb is defined as below
> > CONECT 37 34 38 39 56
> >
> > how do we convert this to the lammps data file format???
>
> you have to be a bit more specific about what is in the .pdb
> file. how many atom types do you have in there? .pdb only has
> the names field.
>
> technically a conversion is possible using the latest VMD beta version.
>
> you would type (on the VMD console window):
>
> mol new filebonds 1
> package require topotools
> topo writelammpsdata
>
> and e-voila. but this way you would not have angle,
> dihedral definitions etc.
>
> cheers,
> axel.
>
> >
> > thanking you
> > vishnu
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> –
> =======================================================================
> Axel Kohlmeyer [email protected] http://www.cmm.upenn.edu
> Center for Molecular Modeling – University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
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>
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cacl2.pdb (813 Bytes)