[gmx-users] Fwd: ion mutation in FEP

-- Forwarded message -- From: SEMRAN İPEK semrani...@gmail.com Date: 2013-05-28 9:22 GMT+03:00 Subject: ion mutation in FEP To: gmx-us...@gromacs.org Dear Users, I have been trying to carry out FEP calculations for a long time for mutation of Glutamine to Aspartic acid using

[gmx-users] two ligand itp file from ACPYPE

Dear Users; Iwould like to run MD calculations using gromacs 4.6.5. My topology file has two ligand. The itp files for these ligands have been generated using *ACPYPE.* *I have followed the instructions given below to include these separate itp files to the topology file. For instance,

[gmx-users] PBC problem after MD

Hi all, I am aware of that this topic has been discussed for many times. However, I need your more guidance whether I am experiencing PBC problem after MD or not. My MD box has enzyme+ligand+coenzyme complex. As I have already wrote to the user list, I am using the force field parameters from

[gmx-users] try

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