virtual_sites3 CHARMM no values for c0 and c1

[Brian Wiley]

Hi,

When I run gmx_MMPBSA with an input topology attached, I get below index error because my topology does not have values for c0 and c2 so there are only words[4] numbers here.  I created the topology with "pdb2gmx ... -ff charmm36 -vsite hydrogens".  Is there a tutorial indicating I should have done something different?

File "/Users/brian/anaconda3/envs/vina/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 683, in _parse_vsites3
    a, b = float(words[5]), float(words[6])
IndexError: list index out of range

[ virtual_sites3 ]

; ai aj ak al funct c0 c1

3 7 1 2 1

4 7 1 2 1

49 45 47 48 1

50 45 47 48 1

...

Brian

[Mario Ernesto]

Seems like you are going to need those parameters, otherwise, the program ends up in error... By the way, keep in mind that we haven't tested gmx_MMPBSA with virtual sites... I don't know if this can conflict down the road with the system preparation...

hth!

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