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

[maria goranovic]

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

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

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 ?

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. Does one have to do the above procedure by
iteratively changing the box size until genbox adds no more solvent ?

Please do not be  ruthless, I am new to gromacs :)

Thank you,


-- 
Maria G.
Technical University of Denmark
Copenhagen
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