I am using an older version (4.5.4) of gromacs. I have restriction to use on my server as I could not speed up with a newer version as i failed to run mpi (which I would try in future).
I want to use TIP4P -Ice model which is not initially in this version. So I added the following
With this, do I need to add a new category to aminoacids.rtp ? . I read in the manual that when we use pdb2gmx, "charges" information is used from .rtp file ; mass information from .atp and force field information from .itp file.
Since charges information for water is also listed in the .itp file (in my case tip4p-ice.itp ) do I again need to add a new category in aminoacids.rtp like SOL2 for this water ??
Where is the charge information for a particular water model used form ?
PS: I am new n naive user of gromacs yet. Any input would be valuable
I want to add :- After adding a category in aminoacids.rtp for my new water system (Tip4p-Ice) , when I use the gromacs command pdb2gmx , I get a topology file that is explicitly listing all my water molecules in [ moleculetype ] one by one
How can I get a topology file that does not explicitly lists every water molecule , its bond and angle information for a new water system ?
Stephane, thanks for answering but I have done this step.
My problem is in the next steps when I try to include this water model in my system.
The .rtp file is only used by pdb2gmx. Typically one adds water in a later step, at which point any model can be specified in the topology, as Stephane has said. The information about the water is then taken directly from whatever .itp file you tell it to.
*.itp (pdm/mol2 file can be processed with ambertools/tleap to obtain topology) and *.gro file (you can generate it with editconf from *.pdb).
This files you have to add to the folder with your source structure files...
Add a corresponding string to the watermodels.dat...
It is a perl script for convertation of amber topology into *.top (rename it to *.itp) and a command line:
./amb2gmx.pl --outname ... --crd *.inpcrd --prmtop *.prmtop
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