Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

On 3/29/20 1:29 AM, Rolly Ng wrote: Hello Justin, Thank you and yes. I went to the paper and it shows the steps for optimization. However, I have the following problems as I tried to follow the tutorial on CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor (1) what

Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

Hello Justin, Thank you and yes. I went to the paper and it shows the steps for optimization. However, I have the following problems as I tried to follow the tutorial on CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor (1) what are these parameters in water_constr.inp?

Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

On 3/25/20 12:52 PM, Rolly Ng wrote: Dear Gromacs Users, I am new to Gromacs and I followed the Protein-Ligand tutorial on the following webpage, http://www.mdtutorials.com/gmx/complex/02_topology.html It works for the example JZ4 but as I changed to another molecule, the str

[gmx-users] How to reduce the penalty of small molecule from CGenFF

Dear Gromacs Users, I am new to Gromacs and I followed the Protein-Ligand tutorial on the following webpage, http://www.mdtutorials.com/gmx/complex/02_topology.html It works for the example JZ4 but as I changed to another molecule, the str file produced by the CGenFF server states very