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
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