[gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Xavier Periole]

On Wed, 3 Oct 2007 19:13:51 +0200
  "maria goranovic" <mariagoranovic at gmail.com> wrote:
> Hi,
> 
> I had a large bilayer in .gro and .top gromacs format files which I
> truncated to make a smaller bilayer, and added some more water molecules,
> using programs other than gromacs. The final output I have is a pdb file
> with complete solvation, and a topology file which I obtained from the
> original top file by simply changing the number of residues of each group in
> the last section. My goal is now to obtain a proper input to the grompp
> program, which is a good .gro and a .top file. The latter I already have.
> 
> pdb2gmx is not working for me with the error:
> 
> %Fatal error:
> %Residue 'DPP' not found in residue topology database
> 

This is because the pdb file truncates the name of your DPPC
(I guess) molecules. just edit the pdb file you have and change
the "DPP " to "DPPC". in vi you can do this by typing:
:1,$ s/DPP /DPPC/

then editconf would allwo you to get a gro file but the pdb should
be ok.

> Q1. How do I add my topology file to the database ?

you have it already.
> 
> Q2. The second question is regarding the use of genbox and editconf. How can
> I specify the box size such that no more solvent is added to the system ?

just add the box size at the end of the gro file.
> 
> Using the following two options adds more solvent to the system, which I do
> not really need
> 
> % editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90
> -bt triclinic -o input.gro -c -center 0 0 0
> % genbox -cp input.gro -o output.gro -cs spc216.gro

no need.
> 
> I chose the box size based on the maximum and minimum coordinates of the
> heavy atoms of the system. Does one have to do the above procedure by
> iteratively changing the box size until genbox adds no more solvent ?

just add the box size at the end of the gro file:
boxX boxX boxZ

> 
> Please do not be  ruthless, I am new to gromacs :)
> 
> Thank you,
> 
> 
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen

-----------------------------------------------------
XAvier Periole - PhD

1- Institute of Molecular Assemblies
      City University of New York - USA
2- Molecular Dynamics-Group
      University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
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