[gmx-users] Re: Inquiry Again.

Albert Sun albert_sun9 at yahoo.com
Fri Aug 1 23:42:01 CEST 2003

Dear Anton and Gmx-users,
If without bonds, I think the top file (as shown in urea.top - manual page 100) will like this:
;name   nrexcl
Urea        3
;nr      type
1    C
2    O
3    NT
4    H
[bonds]  ; no need to input
;ai       aj        funct           b0       kb
  3       4         1            1.0e-01    3.74468e+05
  3       5         1            1.0e-01    3.74468e+05
[angles]  ;  no need to input
[dihedrals];  no need to input
1    1    1000     1000    10000
;include SPC water topology
#include  "spc.itp"
Urea in water
Urea          1
Sol            1000
Appreciate if you could correct it if any mistakes.
Besides, how could we select ' without bonds'  when we do pdb2gmx or by modifying 
.pdb file ?
Thanks in advance.

Anton Feenstra <feenstra at chem.vu.nl> wrote:
Victor Kowalenko wrote:
> Hi Anton,
> I am sending you this e-mail to confirm that the following is all
> I need to get our atomic modelling working in GROMACS as I am not entirely
> sure that this will work.
> First, I need to write a script file that will create *.top file from the
> pdb files. I should mention the format of our pdb files just in case their
> format is unsuitable for GROMACS. They basically go like this:

Whether you need a script depends if you want bonds, without bonds the
.top will be rather trivial and can be written by hand.


x y z 0.00 0.00 
> e.g.
> HETATM 1 Al Al 1 0 0 0 0.00 0.00 Al
> HETATM 2 Cu Cu 2 0 0 1 0.00 0.00 Cu
> etc.
> I think the zeros correspond to velocities or some other units, but they
> are irrelevant for the time being. It is x, y and z coordinates that are 
> important. I would like to know if this format is suitable for GROMACS or
> whether I need to write a script file that extracts only the coordinates.
> The files will have to be altered anyway as the coordinate positions are
> in Angstroms while there is a preference for nm in GROMACS.

Close, but not quite there... This looks like the general .pdb format anyway.
The zeroes should be occupancy and B-factor. Irrelevant for us. The units in
Gromacs files are nm, but .pdb is not a Gromacs file format and the official
PDB file format description insists on angstroms. So, in .pdb you must use
Angtroms, and in .gro nm. It looks like Gromacs will read your files just fine.

> As far as the topology file is concerned, it appears to me that if I elect 
> only to do atom interactions I only need to create a script file that
> creates a topology file with only 2 main parts to it: [atomtypes] and
> [atoms]. That is, it should look like:
> [atomtypes]
> ; specify the various types of atoms in the simulation
> ; atom atomic mass charge epsilon sigma
> Al 26.98 0 LJ_energy in kJ/mol LJ_radius in nm
> Cu 63 0 LJ_energy_2 in kJ/mol LJ_radius_2 in nm
> [atoms]
> ; nr atom type
> 1 Al
> 2 Cu
> 3 Al
> etc.
> where the numbers in the [atoms] correspond to the numbers in the pdb
> files so that GROMACS can get the particle coordinates. 
> I think this is what you are saying below and if this is correct, then
> I see no problem in writing a little script file to read the pdb file
> a structure file. Please inform me as to whether this is correct or
> whether I have missed something. My aim is to create a general script
> file that will variable numbers of particles in the pdb files and place
> them in this format. If the pdb format is no good, then I could create a
> new pdb file with the proper format. 
> Cheers,
> Victor.

Sounds good. You did not include all the obligatory sections above in
your 'example' .top, check the manual for the complete description of
the .top file format.


_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |

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