Hi There, Following is the scenario I am trying for MDS I am using vmd to modify the position of my molecule, and then output from vmd is in .pdb format. for .top file I have generated those files from pdb2gmx and edited them manually as suggested in drug-enzyme tutorial by J E Kerrigan.
Now, I am in doubt weather I can use the .pdb from vmd & .top file for running editconf and genbox followed by MDS ? With Thanks, Vivek
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