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

Xavier Periole X.Periole at rug.nl
Wed Oct 3 23:00:21 CEST 2007

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

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