Hi all
I am new to GROMACS and need help with some issues.
(1) I am trying to run a simulation for glucose in water. The topology file for glucose was generated using AMBER and GLYCAM_06j-1 force field, and then acpype was used to generate the GROMACS topology file. I have then solvated the system, and since the topology file was generated from a program other than GROMACS, I had to manually add the following line to the topology file: #incluse "tip3p.itp", but when proceeded into minimization, I got the following error message: This top-level .itp file has been removed. Edit your topology to include it from your force field directory instead, e.g. "oplsaa.ff/tip3p.itp"'. I am, however, not simulating a protein and not using any of the force fields provided with GROMACS, but I have tried editing the topology file as required and using different types of force fields, but each time I get the following error: [file tip3p.itp, line 7]: Atomtype OW not found. I have also tried using spc water instead of tip3p but without success. How can I resolve this issue?
(2) For the same glucose molecule, I am running another simulation in vacuum. I am using the group cut-off scheme, since verlet needs the periodic boundary conditions to be turned on, which cannot be the case for in vacuum simulation. In each run I get the following note: "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators". Would it be safe just to ignore this note? Or does this have an effect on the accuracy of the calculation?
Your help is highly appreciated.
I don't simulate sugars, but I will try and answer where I can
1) Make sure "include" is spelt correctly (not incluse)
2) From what I have gathered online, the amber glycam is compatible with other amber ff's, and is a stand-alone set of parameters for sugars. Even though you are not simulating protein, you may need to call on a protein amber ff and feed in it's water itp.
For example, this may look like:
#include "amber99sb-ildn.ff/tip3p.itp"
3) Yes, you can ignore this warning
I will reiterate: I don't simulate sugars, so you should look at what others simulating sugars with this forcefield have done, and then try and make some decisions based on that.
Also see here:
http://glycam.org/docs/help/2014/07/02/which-protein-force-fields-are-compatible-with-glycam/
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