GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am performing P-L simulation using the gromacs tutorial.I am facing an fatal error: Topology inclde file “jz4.itp” not found.But as per instruction on tutorial i have added .itp and .prn file in topol.top file.please help to resolve this.
The error means the topology file itself is not present in the working directory.
Respected sir,
Thank you for your quick response.Sir iI have kept the topology file in the same directory still its the same error.(attached)
There is no jz4.itp in your file list in that directory. That is the problem.
sorry to ask sir , but as per tutorial I have not used the charmm36 ff. therefore I have skipped the scrit.tar install step. I have chosen to work with charm27.ff already in the directory so now how do I create a .itp file for it.
The one you have marked above is the protein topology, not the ligand topology i.e. jz4.itp which you need to generate without that your system is not ready to simulate.
If you have taken a different forcefield eg: Amber or gromos, then you need to generate the topology according to that forcefield.
For Amberff you can use acpype and for gromosff you can use ATB server to produce ligand topology, following which you have to update your topol.top and then you will be ready to simulate your system.
Thank sir for your response. As I moved forward with the steps stuck with anther error in NVT minimization.(attached pictures). Please help to resolve sir.
Does your system consist of ions?
You got this error as you don’t have ions in your system, and in you mdp file there is a section of temperature coupling where water and ions are specified, to resolve it add the counter ions with required concentration in your simulation setup before the energy minimization step or remove the ions from temperature coupling if it is not required in your simulation setup.
You have to change this in your nvt.mdp, npt.mdp and md.mdp files, if ions are not there in your simulation setup.
Respected sir,
i Posted my problem to forum but did not got any reply.
I want to use OPLS force filed for my P-L simulations. Therefore as per the instructions in the gromacs tutorial the two files for topology generation need to be processed. But both the servers i.e. [Topolbuild], [TopolGen] and [LigParGen] are not working. Therefore, I request to provide complete steps to execute the OPLS FF with complete topology generation.
Thanks in advance
