From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Fri May 11 2007 - 07:21:20 CDT
SMAHANE CHALABI wrote:
> Dear all,
>
>
> How could I find a pdb, a psf and a topology file of air? I would like
> to create an air box, using VMD I have to enter these files....how to do?
You have to generate these yourself, and they should be pretty simple
since you are dealing with diatomic molecules.
The procedure is the following (I've attached some files for H2S as an
example):
1. Create the topology file, which defines the mass of each atom type,
the charges on each atom and how things are connected together (top_h2s.inp)
2. Create PDB files for each molecule type. You will have to do this
manually following the standard rules for PDB files; it is not difficult
since you only have two atoms (h2s.pdb).
3. Create the parameter file containing the vibrational, bending,
torsion and Lennard-Jones parameters for each interaction (par_h2s.inp).
4. Use Packmol to generate a random initial configuration(h2s_iconfig.inp).
5. Build the system, including the psf file with psfgen (build.tcl).
6. Minimize, equilibrate and run simulation.
Regards,
Jeff
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)577-3810 http://potoff1.eng.wayne.edu ======================================================================
* Parameter file for H2S
* Created by J. Potoff 1/1/07.
BONDS
H S 275.000 1.34
ANGLES
H S H 65.136 92.50 0.00 0.00000
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!adm jr., 5/08/91, suggested cutoff scheme ! NAMD ignores options
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
H 0.000000 0.000000 0.000000 ! H2S Hydrogen
S 0.000000 -0.461000 2.087500 ! H2S Sulfur
* Topology file for H2S
* Parameters from Kamath, Lubna and Potoff, J. Chem. Phys. (2005)
*
27 1
MASS 1 H 1.00800 H ! polar H
MASS 2 S 32.06000 S ! sulfur
RESI H2S 0.00
GROUP
ATOM H1 H 0.19 !
ATOM H2 H 0.19 !
ATOM SH2 S -0.38 !
BOND SH2 H1 SH2 H2
ANGLE H1 SH2 H2
PATCHING FIRS NONE LAST NONE
tolerance 2.0
output h2s_start.pdb
filetype pdb
structure h2s.pdb
number 500
inside cube 0. 0. 0. 62.
end structure
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