Dear All,
I am simulating a system of two sugar molecules in water box. I obtain the structure from glycam website, and bind monosaccharides using bond command in tleap. When running equilibration run, a faced with the error “Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM”. Interestingly (for me, at least), both minimization and heating runs did not give any errors, although I am using sander.MPI for all pre-production runs.
I know this is a known bug in tleap, and also know how to fix it. I wanted to ask if it would be safe to think that bond command worked correctly when I do not get any “bad topology” errors.
With the same bond commands in tleap I have created many systems, and this is the first time that I got such an error.
I use AmberTools15, if it helps.
Best,
Batuhan
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Received on Thu Feb 11 2016 - 12:00:02 PST
