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

[Mark Abraham]

maria goranovic 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:

The purpose of pdb2gmx is to infer topologies from structures. Since you 
have a working topology you don't need this step.

> %Fatal error:
> %Residue 'DPP' not found in residue topology database
> 
> Q1. How do I add my topology file to the database ?

Well, as above, you don't need it. Otherwise, you need to read chapter 5 
of the manual and figure out how it is done.

> 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 ?

I don't understand your objective. If you don't want to add more 
solvent, don't use genbox.

> 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
> 
> I chose the box size based on the maximum and minimum coordinates of the 
> heavy atoms of the system.

Hydrogen takes up volume too... your equilibration will be less 
troublesome if your whole system "fits" at the start of the equilibration.

It sounds like it might be worth your while reading the introductory 
part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea 
what each tool is trying to do. Following a recipe without appreciating 
what you're doing is fine, until you go to change the recipe, which is 
what you're trying to do here. :-)

Mark