Hi,
These things can all be handled by pdb2gmx chain-separation (which
regulates whether the topology generator will expect to make bonds between
residues adjacent in the sequence in the input file) and merging machinery
(if you want your cutout region to be all in the same [moleculetype] or
not),
Okay, now when I did some tests I can explain more precisely what I want to
do.
As I wrote in my other message, I have to cut out some of the amino acids
from my protein.
They are supposed to create an environment around the central amino acid
residue (chromophore in my case).
Because the peptide
If you still need to correct your numbering (for scripting porposes for
example) you can convert your original.gro using editconf and in the final
gro file will be corrected.
On Wed, Feb 3, 2016 at 11:24 AM Dawid das wrote:
> So it turns out that what is important is the order, i.e. when I want
So it turns out that what is important is the order, i.e. when I want
connection
between residues 164 and 165 they need to go in order in my *gro file.
Otherwise there
won't be any bonding in the topology.
Best wishes,
Dawid Grabarek
2016-02-03 10:29 GMT+01:00 Mark Abraham :
> Hi,
>
> Atom numbe
Hi,
Atom numbering is unimportant, but you might see warnings from tools that
recognise it is weird. Residue numbering is important only in that the
value changes when the residue does - it doesn't have to go up by one. Try
it and see ;-)
Mark
On Wed, 3 Feb 2016 10:13 Dawid das wrote:
> Dear G
Dear Gromacs Experts,
Let's assume that I have a *.gro file in a proper format but the number of
atoms and/or
residues is let's say random, e.g. I have coordinates of atoms for residue
87, 95, 96, 88.
What is more, I have let's say 76 atoms in the system, but I start
numbering from 999.
Will I be
